Methods and compositions for modulating T cell and/or B cell activation

ABSTRACT

The present invention provides methods of reducing or enhancing T cell activation and/or B cell activation in a subject, comprising administering to a subject an effective amount of an inhibitor or enhancer, respectively, of Semaphorin 6D (Sema6D) activity on T cells and/or B cells.

STATEMENT OF PRIORITY

This application is a continuation application of, and claims priority to, U.S. application Ser. No. 13/284,341, filed Oct. 28, 2011 issued as U.S. Pat. No. 8,501,677, which is a continuation application of, and claims priority to, U.S. application Ser. No. 12/293,913, filed Mar. 10, 2009, which is a 35 U.S.C. §371 National Phase Application of International Application No. PCT/US2007/007331, filed Mar. 23, 2007, which claims the benefit, under 35 U.S.C. §119(e), of U.S. Provisional Application No. 60/785,310, filed Mar. 23, 2006, the entire contents of each of which are incorporated by reference herein.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, submitted under 37 C.F.R. §1.821, entitled 5470-447TSCT2_ST25.txt, 384,829 bytes in size, generated on Sep. 6, 2013 and filed via EFS-Web, is provided in lieu of a paper copy. This Sequence Listing is hereby incorporated by reference into the specification for its disclosures.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under Grant No. RO1-AI-29564 awarded by the National Institutes of Health. The government has certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates to regulating immune responses by modulating T cell activation and/or B cell activation.

BACKGROUND ART

The immune system is comprised of a complex network of autonomous cells working together to manage a chaotic situation. The regulation of the immune network is equally complex, characterized by hubs of activation control. The dendritic cell (DC) represents one hub of immune control via its unique abilities to regulate activation of CD4⁺ T cells. In turn, CD4⁺ T cells are able to affect the activity of a wide variety of immune cells of both the adaptive and innate categories. During an initial interaction, DCs present antigen (Ag) in the context of MHC class II molecules for recognition by CD4⁺ T cells via their T cell receptor (TCR). Binding of Ag by the TCR represents signal one, but further stimulation derived from costimulatory signals is required for full activation of T cells via DCs. Many co-stimulatory receptor-ligand pairs have been identified between T cells and DCs. The prototypical costimulation interacting pairs on T cells and DCs are CD154-CD40 and CD28-B7 (T-DC respectively). Since their identification, experimental manipulation of these receptors and ligands has proven to be a powerful tool in modulating a wide variety of immune responses ranging from transplant tolerance and autoimmunity to tumor rejection (1-7).

The present invention overcomes previous shortcomings in the art by demonstrating that PlexA1 expressed on DCs and Sema6D expressed on T cells (e.g., CD4⁺ T cells) and on B cells, represent a novel receptor-ligand costimulation pair, capable of regulating immune system activity.

SUMMARY OF THE INVENTION

The present invention provides a method of reducing T cell activation in a subject, comprising administering to the subject an effective amount of an inhibitor of Semaphorin 6D (Sema6D) activity on T cells.

Further provided herein is a method of increasing T cell activation in a subject, comprising administering to the subject an effective amount of an enhancer of Semaphorin 6D (Sema6D) activity on T cells.

In addition, the present invention provides a method of identifying an activated T cell, comprising detecting Sema6D on the surface of the T cell.

The present invention also provides a method of monitoring T cell activation over time, comprising detecting Sema6D on the surface of a T cell over time and measuring changes in the amount of Sema6D on the surface of a T cell over time.

In further embodiments, the present invention provides a method of identifying a substance having the ability to inhibit Sema6D activity, comprising contacting the substance with T cells under conditions wherein Sema6D activity can occur and measuring the amount of Sema6D activity in the presence and in the absence of the substance; whereby a decrease in Sema6D activity in the presence of the substance as compared to the amount of Sema6D activity in the absence of the substance identifies a substance having the ability to inhibit Sema6D activity.

Additionally provided is a method of identifying a substance having the ability to enhance Sema6D activity, comprising contacting the substance with T cells under conditions whereby Sema6D activity can occur and measuring the amount of Sema6D activity in the presence and in the absence of the substance; whereby an increase in Sema6D activity in the presence of the substance as compared to the amount of Sema6D activity in the absence of the substance identifies a substance having the ability to enhance Sema6D activity.

Further provided herein is a method of reducing B cell activation in a subject, comprising administering to a subject in need of reduced B cell activation an effective amount of an inhibitor of Semaphorin 6D (Sema6D) activity on B cells.

In further embodiments, the present invention provides a method of increasing B cell activation in a subject, comprising administering to a subject in need of increased B cell activation an effective amount of an enhancer of Semaphorin 6D (Sema6D) activity on B cells.

Also provided herein is a method of identifying an activated B cell, comprising detecting Sema6D on the surface of the B cell and a method of identifying an activated B cell, comprising detecting messenger RNA encoding Sema6D in the B cell.

Additional embodiments include a method of monitoring B cell activation over time, comprising detecting Sema6D on the surface of a B cell over time and measuring changes in the amount of Sema6D on the surface of a B cell over time, as well as a method of monitoring B cell activation over time, comprising detecting messenger RNA encoding Sema6D in a B cell over time and measuring changes in the amount of messenger RNA encoding Sema6D in the B cell over time.

Additionally provided herein is a method of identifying a substance having an inhibitory effect on Sema6D activity and/or having an inhibitory effect on B cell activation, comprising contacting the substance with B cells under conditions whereby Sema6D activity and/or B cell activation can occur and measuring the amount of Sema6D activity and/or B cell activation in the presence and in the absence of the substance; whereby a decrease in Sema6D activity and/or B cell activation in the presence of the substance as compared to the amount of Sema6D activity and or/B cell activation in the absence of the substance identifies a substance having the ability to inhibit Sema6D activity and/or B cell activation.

Furthermore, the present invention provides a method of identifying a substance having an enhancing effect on Sema6D activity and/or B cell activation, comprising contacting the substance with B cells under conditions whereby Sema6D activity and/or B cell activation can occur and measuring the amount of Sema6D activity and/or B cell activation in the presence and in the absence of the substance; whereby an increase in Sema6D activity and/or B cell activation in the presence of the substance as compared to the amount of Sema6D activity and/or B cell activation in the absence of the substance identifies a substance having the ability to enhance Sema6D activity and/or B cell activation.

It is further contemplated herein that the present invention provides a method of treating a B cell-related disorder and/or a T cell related disorder and/or other white blood cell-related disorder in a subject, comprising administering to the subject a therapeutic amount of an inhibitor of Semaphorin 6D (Sema6D) activity on B cells, T cells and/or other white blood cells.

Various other objectives and advantages of the present invention will become apparent from the following detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows expression of Sema6D mRNA in the immune system. (a) SymAtlas gene array mouse cell and tissue expression of Sema6D mRNA. (b) SymAtlas gene array human cell and tissue expression of Sema6D mRNA. (c) SymAtlas gene array human cancer cell expression of Sema6D mRNA.

DETAILED DESCRIPTION OF THE INVENTION

The present invention will now be described with reference to the following embodiments. As is apparent by these descriptions, this invention can be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the invention to those skilled in the art. For example, features illustrated with respect to one embodiment can be incorporated into other embodiments, and features illustrated with respect to a particular embodiment can be deleted from that embodiment. In addition, numerous variations and additions to the embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.

All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety.

Except as otherwise indicated, standard methods can be used for the production of viral and non-viral vectors, manipulation of nucleic acid sequences, production of transformed cells, and the like according to the present invention. Such techniques are known to those skilled in the art. See, e.g., SAMBROOK et al., MOLECULAR CLONING: A LABORATORY MANUAL 2nd Ed. (Cold Spring Harbor, N.Y., 1989); F. M. AUSUBEL et al. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (Green Publishing Associates, Inc. and John Wiley & Sons, Inc., New York).

The present invention is based on the unexpected discovery that the semaphorin 6D protein on a T cell (e.g., CD4⁺ T cell) surface is a ligand for the Plexin-A1 (PlexA1) receptor protein on antigen-presenting cells, thereby providing the first identification of a ligand for a Plexin-A1 receptor on an immune system cell. Thus, in one embodiment, the present invention provides a method of reducing or inhibiting T cell activation in a subject, comprising administering to the subject (e.g., a subject in need of reduced T cell activation) an effective amount of an inhibitor of Semaphorin 6D (Sema6D) activity on CD4⁺ T cells.

The present invention additionally provides a method of reducing or inhibiting B cell activation in a subject, comprising administering to a subject in need of reduced B cell activation an effective amount of an inhibitor of Semaphorin 6D (Sema6D) activity on B cells.

In the methods of this invention whereby T cell activation and/or B cell activation is reduced or inhibited, a subject of these methods can include a subject having, or at risk of having, an autoimmune disorder or disease, a transplant recipient, a subject having an inflammatory response or at risk of having an inflammatory response, a subject having an allergic response or at risk of having an allergic response and any subject in whom it is desirable to suppress an immune response associated with T cell activation and/or B cell activation, as known in the art.

According to the methods of this invention, an inhibitor of Sema6D activity can be, but is not limited to an antibody or antibody fragment that specifically binds Sema6D, a fusion protein comprising the extracellular domain of the Sema6D protein and an immunoglobulin fragment, an antibody or antibody fragment that specifically binds PlexA1, small molecule mimetics that block the binding of Sema6D to PlexA1 and any substance that inhibits binding of Sema6D to PlexA1 as now known or later identified.

Also included in the methods described herein is a substance that reduces or inhibits Sema6D activity and/or PlexA1 activity at the transcriptional, post-transcriptional, translational and/or post-translational level. For example, —the transcription factor class II transactivator (CIITA) can activate the PlexA1 gene expression in immune dendritic cells (Nature Immunol. 4(9):891-8 2003) and this method of activation is not likely to occur in other tissues with PlexA1 such as neurons and heart cells, since CIITA is not expressed in these other cells. It would be possible to alter CIITA to induce a change in PlexA1 expression predominantly in immune dendritic cells.

In further embodiments of this invention, the inhibitor of Sema6D activity and/or inhibitor of PlexA1 activity is administered in combination (either before, after and/or simultaneously) with another anti-T cell therapeutic and/or anti-B cell therapeutic, either simultaneously, before and/or after administration of the inhibitor of Sema6D activity and/or inhibitor of PlexA1 activity. Nonlimiting examples of an anti-T cell therapeutic include an antibody or fragment thereof or other ligand or fragment thereof that specifically binds and/or inhibits activity of CD3 protein, CD40 protein, B7 family proteins, and/or CD28 family proteins; cyclosporine; FK504; steroids; and/or substances that target MHC-I and/or MHC-II molecules, immunosuppressive drugs, interferons, corticosteroids, azathioprine, cyclophosphamide, etc. Also included are anti-T cell therapeutics that reduce or inhibit CD3 (e.g., OKT®3 monoclonal antibody), CD40, B7 and/or CD28 activity in T cells at the transcriptional, post-transcriptional, translational and/or post-translational level (e.g., an antisense nucleic acid that binds a coding sequence of the Sema6D protein, an interfering RNA that inhibits or suppresses transcription and/or translation of the Sema6D protein, a ribozyme, etc.), therapies that target T cell activation transcription factors, such as inhibitors of IκB kinase (IKK), which would also inhibit the transcription factor, Nuclear Factor kappa light chain enhancer in B cells (NF-κb), or cyclosporine, which inhibits the calcineurin pathway important for the activation of the transcription factor, Nuclear Factor of Activated T cells). Also included are Basiliximab (anti-CD25), Alefacept (LFA3-Ig fusion; blocks CD2), Daclizumab (Anti-CD25), Tysabri (anti-VLA4) and anti-CLA4 Ab. Other inhibitors that can be used in the methods of this invention include but are not limited to Omalizumab (Anti-IgE mab; targets mast cells and basophils) and Lumiliximab (anti-CD23; targets mast cells and basophils).

Nonlimiting examples of an anti-B cell therapeutic include an antibody or fragment thereof or other ligand or fragment thereof that specifically binds and/or inhibits activity of CD20 protein (e.g., Rituximab® monoclonal antibody), immunosuppressive drugs, interferons, corticosteroids, azathioprine, cyclophosphamide, CTLA4-IG (targets CD80/86 on DCs and B cells), Belimumab (targets Blys (BAFF) interactions with receptors on B cells), and Natalizumab or Tysabri (Anti-VLA4; targets T cells and B cells),

Further provided is a method of increasing T cell and/or B cell activation in a subject, comprising administering to the subject (e.g., a subject in need of increased T cell activation and/or increased B cell activation) an effective amount of an enhancer of Semaphorin 6D (Sema6D) activity on T cells and/or B cells.

In the methods provided herein for enhancing T cell activation and/or B cell activation, a subject can be a subject having an infection or at risk of having an infection, a subject having a suppressed immune system or suppressed immune response or at risk of having a suppressed immune system or suppressed immune response, as known in the art. Examples of infections that cause immunosuppression include but are not limited to human immunodeficiency virus infection, cytomegalovirus infection, vaccinia virus infection, and F. tularenesis bacterial infection. Conditions under which immune suppression occurs include severe immunodeficiencies, advanced age, chemotherapy, radiation therapy, irradiation and upon severe burn. In additional embodiments, the enhancer of T cell activation and/or B cell activation can be administered in combination (either before, after and/or simultaneously) with a T cell activation therapeutic and/or a B cell activation therapeutic. Nonlimiting examples of a T cell activation and/or a B cell activation therapeutic of this invention include vaccines such as peptides, DNA and glycoproteins and adjuvants such as toll-like receptor agonists, and the Bacillus Calmette-Guerin.

It is further contemplated herein that T cell activation and/or B cell activation can be reduced, inhibited or enhanced in methods employing ex vivo T cells and/or B cells and/or antigen presenting cells that have been removed from a subject and are subsequently administered to the same subject or a different subject of the same species. Thus, the present invention provides a method of enhancing T cell activation and/or B cell activation, comprising contacting a T cell and/or a B cell with an enhancer of Sema6D activity and/or an enhancer of PlexA1 activity in the presence of an antigen presenting cell having PlexA1 on the surface, under conditions whereby T cell activation and/or B cell activation can occur and then administering the activated T cell and/or activated B cell and/or antigen presenting cell to a subject. Further provided is a method of reducing T cell activation and/or B cell activation, comprising contacting a T cell and/or B cell with an inhibitor of Sema6D activity and/or an inhibitor of PlexA1 activity in the presence of an antigen presenting cell having PlexA1 on the surface, under conditions whereby inhibition of T cell activation and/or inhibition of B cell activation can occur and then administering the T cell and/or B cell and/or antigen presenting cell to a subject.

In other embodiments, the present invention provides a method of identifying an activated T cell or activated B cell, comprising detecting Sema6D on the surface of the T cell or B cell. Further provided herein is a method of identifying an activated T cell or activated B cell, comprising detecting messenger RNA encoding Sema6D in the T cell or B cell.

In methods of this invention wherein Sema6D is detected on the surface of a T cell or a B cell, such detection can be carried out according to methods standard in the art for detecting a protein on the surface of a cell and such methods can be qualitative and/or quantitative. Furthermore, in methods of this invention wherein an amount of messenger RNA encoding Sema6D is detected, such detection can be carried out according to standard methods for detecting nucleic acid in a cell (e.g., polymerase chain reaction (PCR) and other nucleic acid amplification protocols, real-time PCR, RNase protection, in situ hybridization, Northern blots, etc.) and such methods can be qualitative and/or quantitative.

Thus, in some embodiments, the identification of an activated T cell or activated B cell can be carried out by identifying an increase in the amount of Sema6D on the surface of a cell relative to a cell that is not activated. An amount of Sema6D on a T cell or B cell that is not activated can be determined by identifying T cells or B cells that are not activated (as determined by features other than the absence of Sema6D, such as the absence of CD69, CD25, HLA-DR, CD62L, CD154 and/or CD44CD25, IL-2 production, ZAP70, LAT and Lck phosphorylation in T cells) and measuring the amount of Sema6D on the surface of said nonactivated cells to establish a baseline amount of Sema6D. Thus, an activated T cell or activated B cell would be identified as having an amount of Sema6D on the surface that is increased relative to the baseline amount.

Thus, in some embodiments, the increase in Sema6D protein can be an increase of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%. 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 300%, etc., relative to the amount of Sema6D protein on the surface of a nonactivated T cell or nonactivated B cell.

In addition, the increase in Sema6D protein can be at least about 0.1 fold, 0.2 fold, 0.5 fold, 1.0 fold, 1.5 fold, 2.0 fold, 2.5 fold, 3.0 fold, 3.5 fold, 4.0 fold, 4.5 fold, 5.0 fold, 5.5 fold, 6.0 fold, 6.5 fold, 7.0 fold, 7.5 fold, 8.0 fold, 8.5 fold, 9.0 fold, 9.5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, etc., relative to the amount of Sema6D protein on the surface of a nonactivated T cell or nonactivated B cell.

In other embodiments, the increase in Sema6D activity can be an increase of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%. 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 300%, etc., relative to the amount of Sema6D protein on the surface of a nonactivated T cell or nonactivated B cell.

In addition, the increase in Sema6D activity can be at least about 0.1 fold, 0.2 fold, 0.5 fold, 1.0 fold, 1.5 fold, 2.0 fold, 2.5 fold, 3.0 fold, 3.5 fold, 4.0 fold, 4.5 fold, 5.0 fold, 5.5 fold, 6.0 fold, 6.5 fold, 7.0 fold, 7.5 fold, 8.0 fold, 8.5 fold, 9.0 fold, 9.5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, etc., relative to the amount of Sema6D protein on the surface of a nonactivated T cell or nonactivated B cell.

Furthermore, in methods wherein the amount of mRNA encoding Sema6D is measured to identify an activated T cell or activated B cell, a baseline amount of mRNA in a nonactivated T cell or nonactivated B cell can be determined and an activated T cell or activated B cell can be identified by measuring the amount of mRNA relative to the baseline amount.

Thus, the increase in Sema6D mRNA can be of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 300%, etc., relative to the amount of Sema6D mRNA in a nonactivated T cell or nonactivated B cell.

In addition, the increase in Sema6D mRNA can be at least about 0.1 fold, 0.2 fold, 0.5 fold, 1.0 fold, 1.5 fold, 2.0 fold, 2.5 fold, 3.0 fold, 3.5 fold, 4.0 fold, 4.5 fold, 5.0 fold, 5.5 fold, 6.0 fold, 6.5 fold, 7.0 fold, 7.5 fold, 8.0 fold, 8.5 fold, 9.0 fold, 9.5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, etc., relative to the amount of Sema6D mRNA in a nonactivated T cell or nonactivated B cell.

Additionally, in methods of this invention wherein T cell activation and/or B cell activation is inhibited, such inhibition can be detected by identifying a decrease in Sema6D protein on the surface of a T cell and/or B cell and/or by identifying a decrease in mRNA encoding Sema6D protein in a T cell and/or B cell. Such inhibition can be detected by identifying a decrease in Sema6D protein and/or mRNA relative to the amount of Sema6D protein and/or mRNA present in a T cell identified as an activated T cell and/or in a B cell identified as an activate B cell. Typical surface and biochemical activation markers on T cells include but are not limited to CD69, CD25, HLA-DR, CD62L, CD154 and/or the production of IL-2, calcium mobilization, ZAP-70 phosphorylation, LAT phosphorylation, Lck phosphorylation and c-abl kinase activation. Immunologic assays measuring T cell and/or B cell proliferation and cytotoxicity (defined as the ability to kill target cells) can also be used.

Thus, in some embodiments, the inhibition or reduction of T cell activation or B cell activation can be a decrease in Sema6D protein and/or mRNA of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%. 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, etc., relative to the amount of Sema6D protein and/or mRNA in an activated T cell or activated B cell.

In addition, the inhibition or reduction of T cell activation or B cell activation can be a decrease of Sema6D protein and/or mRNA of at least about 0.1 fold, 0.2 fold, 0.5 fold, 1.0 fold, 1.5 fold, 2.0 fold, 2.5 fold, 3.0 fold, 3.5 fold, 4.0 fold, 4.5 fold, 5.0 fold, 5.5 fold, 6.0 fold, 6.5 fold, 7.0 fold, 7.5 fold, 8.0 fold, 8.5 fold, 9.0 fold, 9.5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, etc., relative to the amount of Sema6D protein and/or mRNA in an activated T cell or activated B cell.

The present invention also provides a method of monitoring T cell activation and/or B cell activation over time, comprising detecting Sema6D on the surface of a T cell and/or B cell over time and measuring changes in the amount of Sema6D on the surface of a T cell and/or B cell over time. Additionally provided is a method of monitoring T cell activation and/or B cell activation over time, comprising detecting mRNA encoding Sema6D in a T cell and/or B cell over time and measuring changes in the amount of mRNA encoding Sema6D in the cell over time. Thus a baseline measurement of Sema6D protein and/or mRNA can be performed according to methods known in the art and as described herein and measurements of Sema6D protein and/or mRNA can be carried out at any time interval (e.g., minutes, hours, days, etc.) and under conditions whereby T cell activation and/or B cell activation can be modulated. Changes in the amount of Sema6D protein and/or mRNA can be detected, whereby an increase or decrease in the amount of Sema6D protein and/or mRNA can identify an increase or decrease, respectively in the activation of a T cell and/or B cell over time.

The present invention further provides screening methods, including a method of identifying a substance having the ability to inhibit Sema6D activity, comprising contacting the substance with T cells and/or B cells expressing Sema6D under conditions whereby Sema6D activity can occur and measuring the amount of Sema6D activity in the presence and in the absence of the substance; whereby a decrease in Sema6D activity in the presence of the substance as compared to the amount of Sema6D activity in the absence of the substance identifies a substance having the ability to inhibit Sema6D activity.

Further provided herein is a method of identifying a substance having the ability to enhance Sema6D activity, comprising contacting the substance with T cells and/or B cells expressing Sema6D under conditions whereby Sema6D activity can occur and measuring the amount of Sema6D activity in the presence and in the absence of the substance; whereby an increase in Sema6D activity in the presence of the substance as compared to the amount of Sema6D activity in the absence of the substance identifies a substance having the ability to enhance Sema6D activity.

In the screening methods of this invention, Sema6D activity indicates activation of T cells, as determined by measurement of T cell activation markers such as CD25, CD69, CD62L, CD154, CD44, HLA-DR, IL-2 production, calcium mobilization, phosphorylation of LAT, ZAP70, lck, c-Abl etc., in response to a substance that can bind and activate through the Sema6D molecule. An example would be a fusion protein consisting of the extramembrane domain of PlexA1 coupled with the Fc portion of immunoglobulin as described herein.

Sema6D activity can be measured by, for example, identifying the T cell and/or B cell activation status of a T cell and/or B cell in the absence of a test substance and measuring the T cell and/or B cell activation status of the T cell and/or B cell in the presence of the substance, whereby an increase in T cell and/or B cell activation in the presence of the substance identifies the substance as having the ability to enhance Sema6D activity and whereby a decrease in T cell and/or B cell activation in the presence of the substance identifies a substance having the ability to inhibit Sema6D activity. The activation status of a T cell can be measured by methods standard in the art, including but not limited to, measuring an increase in the production and/or expression of CD69, CD25, HLA-DR, CD62L, CD154 and/or CD44, either singly or in any combination, in the T cell, according to art-known methods. T cell activation status can also be determined by employing art-known methods for detecting cytotoxic T cell responses, T helper responses and/or IL-2 production. The activation status of a B cell can be measured by methods standard in the art.

In some embodiments, the screening methods of this invention can include the step of contacting the T cells and/or B cells with a known inhibitor of Sema6D activity, such as an antibody that specifically binds a Sema6D protein or a fusion protein of this invention comprising the extracellular domain of a Sema6D protein and an immunoglobulin fragment and establishing a baseline amount of T cell and/or B cell activation and then contacting the T cell and/or B cell with the substance to be screened and identifying a change in the T cell and/or B cell activation status to identify a substance that either inhibits or enhances Sema6D activity. Typical surface and biochemical activation markers on T cells include but are not limited to CD69, CD25, HLA-DR, CD62L, CD154 and/or the production of IL-2, calcium mobilization, ZAP-70 phosphorylation, LAT phosphorylation, and Lck phosphorylation. T cell proliferation and cytotoxicity (defined as the ability to kill target cells) can also be measured. Sema6D activity can be measured by the methods described herein.

In some embodiments of this invention, substances can be screened for the ability to inhibit or enhance Sema6D activity by affecting the ability of Sema6D to bind PlexA1. This inhibition or enhancement of binding activity can be detected by any of a variety of art-recognized methods for evaluating binding activity. As one example, the substance to be tested and a PlexA1 protein or an active fragment thereof can be contacted in the presence of T cells and/or B cells having Sema6D on the surface. The amount of binding of PlexA1 to the cells in the presence of the substance and the amount of binding of PlexA1 to the cells in the absence of the substance can be determined and a decrease or increase in the amount of binding in the presence of the substance identifies the substance as having the ability to inhibit or enhance binding, respectively and thus inhibit or enhance Sema6D activity, respectively.

In some embodiments, binding of the PlexA1 protein to a T cell or B cell can be measured by attaching a detectable moiety to the PlexA1 polypeptide or fragment (e.g., a fluorescence moiety, histochemically detectable moiety, radioactive moiety, etc.). The amount of detectable moiety can be measured in the presence and absence of the substance to be tested and the amounts can be compared to determine inhibition or enhancement. T cell activation can be measured by methods not limited to the following: detection and/or quantitation of cell surface markers such as CD69, CD25, HLA-DR, CD62L, CD154 and/or the production of IL-2, calcium mobilization, ZAP-70 phosphorylation, LAT phosphorylation, Lck phosphorylation; NF-κB activation, MEK activation, NFAT activation, Ap-1 activation; T cell proliferation and cytotoxicity (defined as the ability to kill target cells).

Substances suitable for screening according to the above methods include small molecules, natural products, peptides, nucleic acids, etc. Sources for compounds include natural product extracts, collections of synthetic compounds, and compound libraries generated by combinatorial chemistry. Libraries of compounds are well known in the art. Small molecule libraries can be obtained from various commercial entities, for example, SPECS and BioSPEC B.V. (Rijswijk, the Netherlands), Chembridge Corporation (San Diego, Calif.), Comgenex USA Inc., (Princeton, N.J.), Maybridge Chemical Ltd. (Cornwall, UK), and Asinex (Moscow, Russia). One representative example is known as DIVERSet™, available from ChemBridge Corporation, 16981 Via Tazon, Suite G, San Diego, Calif. 92127. DIVERSet™ contains between 10,000 and 50,000 drug-like, hand-synthesized small molecules. The compounds are pre-selected to form a “universal” library that covers the maximum pharmacophore diversity with the minimum number of compounds and is suitable for either high throughput or lower throughput screening. For descriptions of additional libraries, see, for example, Tan et al. “Stereoselective Synthesis of Over Two Million Compounds Having Structural Features Both Reminiscent of Natural Products and Compatible with Miniaturized Cell-Based Assays” Am. Chem Soc. 120, 8565-8566, 1998; Floyd et al. Prog Med Chem 36:91-168, 1999. Numerous libraries are commercially available, e.g., from AnalytiCon USA Inc., P.O. Box 5926, Kingwood, Tex. 77325; 3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Suite 104, Exton, Pa. 19341-1151; Tripos, Inc., 1699 Hanley Rd., St. Louis, Mo., 63144-2913, etc. In certain embodiments of the invention the methods are performed in a high-throughput format using techniques that are well known in the art, e.g., in multiwell plates, using robotics for sample preparation and dispensing, etc. Representative examples of various screening methods may be found, for example, in U.S. Pat. Nos. 5,985,829, 5,726,025, 5,972,621, and 6,015,692. The skilled practitioner will readily be able to modify and adapt these methods as appropriate.

The present invention further provides compositions, such as a fusion protein comprising the extracellular domain of a Sema6D protein or an active portion or fragment thereof and any active or functional fragment of an immunoglobulin molecule, as would be well known in the art. Also provided is a fusion protein comprising a transmembrane domain or an active portion or fragment thereof of a Sema6D protein and/or an intracellular domain or an active portion or fragment thereof of a Sema6D protein and an active or functional fragment of an immunoglobulin molecule. The present invention further provides a composition comprising a fusion protein of this invention in a pharmaceutically acceptable carrier. Additionally provided is a composition comprising an antibody or other ligand that specifically binds a Sema6D protein in a pharmaceutically acceptable carrier. Further provided herein is a nucleotide sequence encoding a fusion protein of this invention, which nucleotide sequence can be present in a composition comprising a pharmaceutically acceptable carrier. These compositions can be delivered to a subject of this invention in methods as described herein and in methods of treating disorders and diseases as described herein associated with increased or decreased T cell and/or B cell activation.

Thus, in further embodiments, the present invention provides a method of treating a T-cell-related disorder, B cell-related disorder and/or other white blood cell related disease or disorder in a subject, comprising administering to the subject a therapeutic amount of an inhibitor of Semaphorin 6D (Sema6D) activity on T cells, B cells and/or other white blood cells.

Nonlimiting examples of the diseases and disorders that can be treated according to the methods of this invention include but are not limited to leukemia (e.g., lymphoblastic leukemia, chronic myelogenous leukemia; promyelocytic leukemia, etc.; FIG. 1), lymphoma (e.g., B cell lymphomas, T cell lymphomas, Burkitts lymphoma, etc.), autoimmune diseases and disorders, inflammatory disorders and diseases, transplant rejection, psoriasis, asthmatic and allergic disorders and any combination thereof.

Nonlimiting examples of autoimmune disorders and diseases that can be treated and/or prevented by the methods of this invention include arthritis (e.g., rheumatoid arthritis or RA), multiple sclerosis (MS), diabetes (e.g., insulin dependent diabetes mellitus or IDDM), systemic lupus erythematosus (SLE), allergic reactions, asthmatic reaction, myasthenia gravis, Crohns' disease, regional enteritis, vasculitis, ulcerative colitis, Sjogren's syndrome, ankylosing spondylitis, polymyositis and any other autoimmune disorder now known or later identified.

An inflammatory disease or disorder of this invention can include but is not limited to inflammation of any organ, e.g., skin, heart, gastrointestinal tract, central nervous system, liver, pancreas, ovary, lung, eye, ear, throat, etc., such as, e.g., in psoriasis and general tissue fibrosis.

Additionally provided is a method of reducing the likelihood of transplant rejection (or increasing the likelihood of successful transplantation) in a transplant recipient, comprising administering to the transplant recipient an effective amount of an inhibitor of T cell and/or B cell activation of this invention. The reduction in the likelihood of transplant rejection or increase in the likelihood of successful transplantation is in comparison to the likelihood of transplant rejection or likelihood of successful transplantation in a transplant recipient that did not receive an inhibitor of T cell and/or B cell activation, as such likelihood would be known and/or determined according to art-known standards. Furthermore, the inhibitor of these methods can be administered to the transplant recipient at any time relative to the transplantation (i.e., before, after and/or simultaneously, in any combination).

In further embodiments, the present invention provides nucleic acids that inhibit T cell and/or B cell activation and nucleic acids that enhance T cell and/or B cell activation. These nucleic acids can be present in a composition comprising a pharmaceutically acceptable carrier. These nucleic acids can be present in vectors, plasmids, and/or other vehicles for delivery of nucleic acids to cells to carry out the methods of this invention, as described herein. These nucleic acids can encode inhibitors and enhancers of T cell and/or B cell activation and/or these nucleic acids can act directly to inhibit or enhance T cell and/or B cell activation, for example, by inhibiting or enhancing Sema6D activity at the nucleic acid level.

Also provided herein is a method of treating a disorder or disease associated with decreased T cell and/or B cell activation, comprising administering to the subject an effective amount of an enhancer of T cell and/or B cell activation as described herein.

In the methods provided herein for enhancing T cell and/or B cell activation in a subject, such an enhancement can be identified by comparison with T cell and/or B cell activation in a subject that did not receive the enhancer of this invention. Such comparative studies can be carried out according to well known protocols in the art for detecting and/or measuring T cell and/or B cell activation, and as described herein.

Thus, the present invention further provides a method of initiating, inducing and/or enhancing a T cell-mediated immune response and/or a B cell-mediated immune response in a subject, comprising administering to the subject an effective amount of an enhancer of Semaphorin 6D (Sema6D) activity on T cells and/or B cells.

The subject of this invention can be any subject in need of the immunomodulating effects of the methods of this invention. Such a subject can be any type of animal that is susceptible to diseases and disorders associated with increased T cell and/or B cell activation or decreased T cell and/or B cell activation and/or that can be treated by increasing or decreasing T cell and/or B cell activation according to the methods of this invention, as well as any animal to whom the compositions of this invention can be administered according to the methods of this invention. For example, an animal of this invention can be a mammal, a bird or a reptile. In certain embodiments, the subject of this invention is a human.

As noted above, the compositions of this invention can be administered to a cell of a subject or to a subject either in vivo or ex vivo. For administration to a cell of the subject in vivo, as well as for administration to the subject, the compositions of this invention can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, subcutaneous injection, transdermally, extracorporeally, topically, by transdermal patch, or the like.

The exact amount of the composition required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the particular composition used, its mode of administration, the condition being treated and the like. Thus, it is not possible to specify an exact amount for every composition of this invention. However, an effective amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.

As an example, one or more doses of between about 0.1 μg/kg and about 1000 mg/kg of an inhibitor and/or biologically active fragment of this invention can be administered orally and/or parenterally to a subject in whom it is desirable to decrease T cell activation, at hourly, daily and/or weekly intervals until an evaluation of the subject's clinical parameters indicate that the subject's condition has improved and/or the subject demonstrates the desired response.

If ex vivo methods are employed, cells or tissues can be removed and maintained outside the subject's body according to standard protocols well known in the art. The compositions of this invention can be introduced into the cells via known mechanisms for uptake of materials into cells (e.g., phagocytosis, pulsing onto class I MHC-expressing cells, liposomes, etc.). The cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or transplanted back into the same subject or a different subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.

The pharmaceutical compositions of this invention include those suitable for oral, rectal, topical, inhalation (e.g., via an aerosol) buccal (e.g., sub-lingual), vaginal, parenteral (e.g., subcutaneous, intramuscular, intradermal, intraarticular, intrapleural, intraperitoneal, intracerebral, intraarterial, or intravenous), topical (i.e., both skin and mucosal surfaces, including airway surfaces) and transdermal administration, although the most suitable route in any given case will depend, as is well known in the art, on such factors as the species, age, gender and overall condition of the subject, the nature and severity of the condition being treated and/or on the nature of the particular composition (i.e., dosage, formulation) that is being administered.

Pharmaceutical compositions suitable for oral administration can be presented in discrete units, such as capsules, cachets, lozenges, or tables, each containing a predetermined amount of the composition of this invention; as a powder or granules; as a solution or a suspension in an aqueous or non-aqueous liquid; or as an oil-in-water or water-in-oil emulsion. Oral delivery can be performed by complexing a composition of the present invention to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers include plastic capsules or tablets, as known in the art. Such formulations are prepared by any suitable method of pharmacy, which includes the step of bringing into association the composition and a suitable carrier (which may contain one or more accessory ingredients as noted above). In general, the pharmaceutical composition according to embodiments of the present invention are prepared by uniformly and intimately admixing the composition with a liquid or finely divided solid carrier, or both, and then, if necessary, shaping the resulting mixture. For example, a tablet can be prepared by compressing or molding a powder or granules containing the composition, optionally with one or more accessory ingredients. Compressed tablets are prepared by compressing, in a suitable machine, the composition in a free-flowing form, such as a powder or granules optionally mixed with a binder, lubricant, inert diluent, and/or surface active/dispersing agent(s). Molded tablets are made by molding, in a suitable machine, the powdered compound moistened with an inert liquid binder.

Pharmaceutical compositions suitable for buccal (sub-lingual) administration include lozenges comprising the composition of this invention in a flavored base, usually sucrose and acacia or tragacanth; and pastilles comprising the composition in an inert base such as gelatin and glycerin or sucrose and acacia.

Pharmaceutical compositions of this invention suitable for parenteral administration can comprise sterile aqueous and non-aqueous injection solutions of the composition of this invention, which preparations are preferably isotonic with the blood of the intended recipient. These preparations can contain anti-oxidants, buffers, bacteriostats and solutes, which render the composition isotonic with the blood of the intended recipient. Aqueous and non-aqueous sterile suspensions, solutions and emulsions can include suspending agents and thickening agents. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.

The compositions can be presented in unit\dose or multi-dose containers, for example, in sealed ampoules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, saline or water-for-injection immediately prior to use.

Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules and tablets of the kind previously described. For example, an injectable, stable, sterile composition of this invention in a unit dosage form in a sealed container can be provided. The composition can be provided in the form of a lyophilizate, which can be reconstituted with a suitable pharmaceutically acceptable carrier to form a liquid composition suitable for injection into a subject. The unit dosage form can be from about 0.1 μg to about 10 grams of the composition of this invention. When the composition is substantially water-insoluble, a sufficient amount of emulsifying agent, which is physiologically acceptable, can be included in sufficient quantity to emulsify the composition in an aqueous carrier. One such useful emulsifying agent is phosphatidyl choline.

Pharmaceutical compositions suitable for rectal administration are preferably presented as unit dose suppositories. These can be prepared by admixing the composition with one or more conventional solid carriers, such as for example, cocoa butter and then shaping the resulting mixture.

Pharmaceutical compositions of this invention suitable for topical application to the skin preferably take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers that can be used include, but are not limited to, petroleum jelly, lanoline, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof. In some embodiments, for example, topical delivery can be performed by mixing a pharmaceutical composition of the present invention with a lipophilic reagent (e.g., DMSO) that is capable of passing into the skin.

Pharmaceutical compositions suitable for transdermal administration can be in the form of discrete patches adapted to remain in intimate contact with the epidermis of the subject for a prolonged period of time. Compositions suitable for transdermal administration can also be delivered by iontophoresis (see, for example, Pharmaceutical Research 3:318 (1986)) and typically take the form of an optionally buffered aqueous solution of the composition of this invention. Suitable formulations can comprise citrate or bis\tris buffer (pH 6) or ethanol/water and can contain from 0.1 to 0.2M active ingredient.

Furthermore, the compositions of this invention can be administered orally, intranasally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like. In the methods described herein which include the administration and uptake of exogenous DNA into the cells of a subject (i.e., gene transduction or transfection), the nucleic acids of the present invention can be in the form of naked DNA or the nucleic acids can be in a vector for delivering the nucleic acids to the cells for expression of the polypeptides and/or fragments of this invention. The vector can be a commercially available preparation or can be constructed in the laboratory according to methods well known in the art.

Delivery of a nucleic acid or vector to cells can be via a variety of mechanisms. As one example, delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, Md.), SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison, Wis.), as well as other liposomes developed according to procedures standard in the art. In addition, the nucleic acid or vector of this invention can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, Calif.) as well as by means of a SONOPORATION machine (ImaRx Pharmaceutical Corp., Tucson, Ariz.).

As one example, vector delivery can be via a viral system, such as a retroviral vector system, which can package a recombinant retroviral genome. The recombinant retrovirus can then be used to infect and thereby deliver to the infected cells nucleic acid encoding the polypeptide and/or fragment of this invention. The exact method of introducing the exogenous nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors. Other techniques are widely available for this procedure including the use of adenoviral vectors, alphaviral vectors, adeno-associated viral (AAV) vectors, lentiviral vectors, pseudotyped retroviral vectors and vaccinia viral vectors, as well as any other viral vectors now known or developed in the future. Physical transduction techniques can also be used, such as liposome delivery and receptor-mediated and other endocytosis mechanisms. This invention can be used in conjunction with any of these or other commonly used gene transfer methods.

As one example, if the nucleic acid of this invention is delivered to the cells of a subject in an adenovirus vector, the dosage for administration of adenovirus to humans can range from about 10⁷ to 10⁹ plaque forming units (pfu) per injection, but can be as high as 10¹², 10¹⁵ and/or 10²⁰ pfu per injection.

In some embodiments, a subject will receive a single injection of a viral vector comprising a nucleic acid of this invention. If additional injections are necessary, they can be repeated at daily/weekly/monthly intervals for an indefinite period and/or until the efficacy of the treatment has been established. As set forth herein, the efficacy of treatment can be determined by evaluating the symptoms and clinical parameters described herein and/or by detecting a desired immunological response.

The exact amount of the nucleic acid or vector required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every nucleic acid or vector. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.

Further provided are isolated nucleic acids comprising, consisting essentially of and/or consisting of nucleotide sequences that encode the proteins and fragments of this invention. In particular, the present invention provides a fusion protein comprising, consisting essentially of, and/or consisting of the amino acid sequence of SEQ ID NO:2

(Sema6D-Ig: primary amino acid sequence (886 aa) (MGFLLLWFCVLFLLVSRLRAVSFPEDDEPLNTVDYHYSRQYPVFRGRPSGNESQHRL DFQLMLKIRDTLYIAGRDQVYTVNLNEIPQTEVIPSKKLTWRSRQQDRENCAMKGKH KDECHNFIKVFVPRNDEMVFVCGTNAFNPMCRYYRLRTLEYDGEEISGLARCPFDAR QTNVALFADGKLYSATVADFLASDAVIYRSMGDGSALRTIKYDSKWIKEPHFLHAIE YGNYVYFFFREIAVEHNNLGKAVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNC SVPGDSFFYFDVLQSITDIIQINGIPTVVGVFTTQLNSIPGSAVCAFSMDDIEKVFKGRF KEQKTPDSVWTAVPEDKVPKPRPGCCAKHGLAEAYKTSIDFPDDTLAFIKSHPLMDS AVPPIADEPWFTKTRVRYRLTAIEVDRSAGPYQNYTVIFVGSEAGVVLKVLAKTSPFS LNDSVLLEEIEAYNPAKCSAESEEDRKVVSLQLDKDHHALYVAFSSCVVRIPLSRCER YGSCKKSCIASRDPYCGWLSQGVCERVTLGMLPGGYEQDTEYGNTAHLGDCHDME VSSSSVTTVASSPEITSKVIDTWRPKLTSSRKFVVQDDPNTSDFTDTISGIPKGVRWEV QSGESNQMVHMNVLITCVFAA): Sema6D seq (652 aa) (GSEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDP EVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSN KALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWES NGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQK SLSLSPGK): Ig seq

Additionally provided is a nucleic acid comprising, consisting essentially of, and/or consisting of a nucleotide sequence that encodes an amino acid sequence comprising, consisting essentially of, and/or consisting of the amino acid sequence or a biologically active fragment of the amino acid sequence of SEQ ID NO:2 above. In a particular embodiment, the nucleic acid of this invention comprises the nucleotide sequence of SEQ ID NO:1:

(GCCACCCATGGGGTTCC TTCTGCTTTG GTTCTGCGTG CTGTTCCTTC TGGTCTCCAG GTTACGGGCGGTCAGCTTCC CAGAAGACGA TGAGCCCCTC AACACGGTTG ACTATCACTA TTCAAGGCAATATCCGGTTT TTAGAGGACG CCCTTCAGGC AACGAATCGC AGCACAGGCT GGACTTTCAGCTGATGTTGA AAATTCGAGA CACACTTTAT ATTGCTGGCA GGGATCAAGT CTATACAGTGAACTTAAATG AAATCCCCCA AACAGAGGTG ATACCAAGCA AGAAGCTGAC GTGGAGGTCCAGACAGCAGG ATCGAGAAAATTGTGCTATG AAAGGCAAGC ATAAAGATGA ATGCCACAACTTCATCAAAG TCTTTGTCCC AAGAAATGAT GAGATGGTTT TTGTCTGTGG TACCAATGCTTTCAACCCGA TGTGCAGATA CTATAGGTTG AGAACGTTAG AGTATGATGG GGAAGAAATTAGTGGCCTGG CACGATGCCC GTTTGATGCC CGACAAACCA ATGTCGCCCT CTTTGCTGATGGAAAACTCT ATTCTGCCAC AGTGGCTGAT TTCCTGGCCA GTGATGCTGT CATTTACAGAAGCATGGGAG ATGGATCTGC CCTTCGCACA ATAAAATACG ATTCCAAGTG GATCAAAGAACCACACTTCC TTCATGCCAT AGAATATGGA AACTATGTCT ATTTCTTCTT CAGAGAAATCGCCGTGGAAC ATAATAACTT AGGCAAGGCT GTGTATTCCC GCGTGGCTCG CATTTGTAAAAACGACATGG GTGGCTCACA GCGGGTCCTG GAGAAACACT GGACTTCCTT CCTTAAGGCTCGGCTGAACT GCTCCGTTCC TGGAGATTCC TTTTTCTACT TCGACGTCCT GCAGTCTATAACAGACATAA TCCAAATCAA TGGCATCCCC ACTGTGGTTG GGGTCTTCAC CACACAGCTCAACAGCATTC CTGGTTCTGC AGTCTGTGCC TTTAGCATGG ACGACATTGA GAAAGTGTTCAAAGGGCGGT TCAAAGAGCA GAAAACCCCA GACTCTGTTT GGACAGCAGT TCCCGAAGACAAAGTACCAA AACCAAGGCC TGGCTGTTGT GCCAAACACG GCCTCGCAGA AGCTTACAAGACCTCCATCG ACTTTCCAGA TGACACCCTG GCTTTCATCA AGTCCCACCC GCTGATGGACTCTGCCGTCC CACCCATTGC CGATGAGCCC TGGTTCACAA AGACACGGGT CAGGTACAGGTTGACAGCCA TCGAAGTGGA CCGTTCAGCA GGGCCATACC AAAACTACAC AGTCATCTTTGTTGGCTCTG AAGCTGGCGT GGTACTTAAA GTTTTGGCAA AGACCAGTCC TTTCTCTCTGAATGACAGTG TATTACTCGA AGAGATTGAA GCTTATAACC CAGCCAAGTG CAGCGCCGAGAGTGAGGAGG ACAGAAAGGT GGTCTCATTA CAGCTGGACA AGGATCACCA TGCTTTATACGTGGCCTTCT CTAGCTGCGT GGTCCGCATC CCCCTCAGCC GCTGTGAGCG CTACGGATCGTGTAAAAAGT CTTGCATTGC ATCACGTGAC CCGTACTGTG GTTGGTTAAG CCAGGGAGTTTGTGAGAGAG TGACCCTAGG GATGCTCCCT GGAGGATATG AGCAGGACACGGAGTACGGCAACACAGCCC ACCTAGGGGA CTGCCACGAC ATGGAGGTAT CCTCATCTTC TGTTACCACTGTGGCAAGTA GCCCAGAAAT TACATCTAAA GTGATTGATA CCTGGAGACC TAAACTGACGAGCTCCCGGA AATTTGTAGT TCAAGATGAC CCAAATACTT CTGATTTTAC TGATACTATATCAGGTATCC CAAAGGGTGT ACGGTGGGAA GTCCAGTCTG GAGAATCCAA TCAGATGGTCCACATGAATG TCCTCATCAC CTGCGTGTTT GCCGCTGGAT CCGAGCCCAA ATCTTGTGACA AAACTCACAC ATGCCCACCG TGCCCAGCA CTGAACTCCT GGGGGGACCG TCAGTCTTCC TCTTCCCCCC  AAAACCCAAG GACACCCTCA TGATCTCCCG GACCCCTGAG GTCACATGCG TGGTGGTGGA CGTGAGCCAC GAAGACCCTGAGGTCAAGTT CAACTGGTAC GTGGACGGCG TGGAGGTGCA TAATGCCAAG ACAAAGCCGCGGGAGGAGCA GTACAACAGC ACGTACCGTG TGGTCAGCGT CCTCACCGTC CTGCACCAGGACTGGCTGAA TGGCAAGGAG TACAAGTGCA AGGTCTCCAA CAAAGCCCTC CCAGCCCCCATCGAGAAAAC CATCTCCAAA GCCAAAGGGC AGCCCCGAGA ACCACAGGTG TACACCCTGCCCCCATCCCG GGATGAGCTG ACCAAGAACC AGGTCAGCCT GACCTGCCTG GTCAAAGGCTTCTATCCCAG CGACATCGCC GTGGAGTGGG AGAGCAATGG GCAGCCGGAG AACAACTACAAGACCACGCC TCCCGTGCTG GACTCCGACG  GCTCCTTCTT CCTCTACAGC AAGCTCACCGTGGACAAGAG CAGGTGGCAG CAGGGGAACG TCTTCTCATG CTCCGTGATG CATGAGGCTCTGCACAACCA CTACACGCAG AAGAGCCTCT CCCTGTCTCC GGGTAAATGA).

Further provided herein is a nucleic acid that is the complement of each and any of the nucleic acids of this invention.

A variety of protocols for detecting the presence of and/or measuring the amount of Sema6D protein, using, e.g., polyclonal and/or monoclonal antibodies specific for the Sema6D protein, are known in the art. Examples of such protocols include, but are not limited to, enzyme immunoassays (EIA), agglutination assays, immunoblots (Western blot; dot/slot blot, etc.), radioimmunoassays (RIA), immunodiffusion assays, chemiluminescence assays, antibody library screens, expression arrays, enzyme-linked immunosorbent assays (ELISA), radioimmunoassays (RIA), immunoprecipitation, Western blotting, competitive binding assays, immunofluorescence, immunohistochemical staining precipitation/flocculation assays and fluorescence-activated cell sorting (FACS). These and other assays are described, among other places, in Hampton et al. (Serological Methods, a Laboratory Manual, APS Press, St Paul, Minn. (1990)) and Maddox et al. (J. Exp. Med. 158:1211-1216 (1993)).

Furthermore, a number of assays for identification, detection and/or amplification of nucleic acid sequences (e.g., Sema6D mRNA) are well known in the art. For example, various protocols can be employed in the methods of this invention to amplify nucleic acid. As used herein, the term “oligonucleotide-directed amplification procedure” refers to template-dependent processes that result in an increase in the concentration of a specific nucleic acid molecule relative to its initial concentration, or in an increase in the concentration of a detectable signal, such as amplification. As used herein, the term “oligonucleotide directed mutagenesis procedure” is intended to refer to a process that involves the template-dependent extension of a primer molecule. The term “template dependent process” refers to nucleic acid synthesis of a RNA or a DNA molecule wherein the sequence of the newly synthesized strand of nucleic acid is dictated by the well-known rules of complementary base pairing. Typically, vector mediated methodologies involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided in U.S. Pat. No. 4,237,224 (incorporated herein by reference in its entirety). Nucleic acids, used as a template for amplification methods can be isolated from cells according to standard methodologies (Sambrook et al., 1989). The nucleic acid can be genomic DNA or fractionated or whole cell RNA. Where RNA is used, it may be desired to convert the RNA to a complementary DNA. In one embodiment, the RNA can be whole cell RNA and is used directly as the template for amplification.

Pairs of primers that selectively hybridize to nucleic acids corresponding to the Sema6D gene or coding sequence are contacted with the nucleic acid under conditions that permit selective hybridization. The term “primer,” as defined herein, is meant to encompass any nucleic acid that is capable of priming the synthesis of a nascent nucleic acid in a template dependent process. Typically, primers are oligonucleotides from ten to twenty bases in length, but shorter (e.g., 6, 7, 8, or 9 bases) or longer (e.g., 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50 bases) sequences can be employed. Primers can in double-stranded or single-stranded form, although the single-stranded form is commonly used.

Once hybridized, the nucleic acid: primer hybridization complex is contacted with one or more enzymes that facilitate template-dependent nucleic acid synthesis. Multiple rounds of amplification, also referred to as “cycles,” are conducted until a sufficient amount of amplification product is produced.

Next, the amplification product is detected. In some embodiments, the detection can be performed by visual means. Alternatively, the detection can involve indirect identification of the product via chemiluminescence, radioactive scintigraphy of incorporated radiolabel or fluorescence or chemiluminescence label or even via a system using electrical or thermal impulse signals (e.g., Affymax technology).

A number of template dependent processes are available to amplify the sequences present in a given template sample. One of the best-known amplification methods is the polymerase chain reaction (referred to as PCR), which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, each incorporated herein by reference in its entirety.

Briefly, in PCR, two primer sequences are prepared that are complementary to regions on opposite complementary strands of the target sequence. An excess of deoxynucleoside triphosphates is added to a reaction mixture along with a DNA polymerase, e.g., a Taq polymerase. If the particular target sequence is present in a sample, the primers will bind to the target sequence and the polymerase will cause the primers to be extended along the sequence by adding on nucleotides. By raising and lowering the temperature of the reaction mixture, the extended primers will dissociate from the target sequence to form reaction products, excess primers will bind to the target sequence and to the reaction products and the process is repeated.

A reverse transcriptase PCR amplification procedure can be performed in order to quantify the amount of mRNA amplified. Methods of reverse transcribing RNA into cDNA are well known in the art (e.g., Sambrook et al., 1989). Alternative methods for reverse transcription employ thermostable, RNA-dependent DNA polymerases. These methods are described, for example, in PCT Publication No. WO 90/07641, filed Dec. 21, 1990, incorporated herein by reference in its entirety. Polymerase chain reaction methodologies are well known in the art.

Another method for nucleic acid amplification is the ligase chain reaction (“LCR”), disclosed in Eur. Pat. Appl. No. 320308, incorporated herein by reference in its entirety. In LCR, two complementary probe pairs are prepared and in the presence of the target sequence, each pair will bind to opposite complementary strands of the target such that they abut. In the presence of a ligase, the two probe pairs will link to form a single unit. By temperature cycling, as in PCR, bound ligated units dissociate from the target and then serve as “target sequences” for ligation of excess probe pairs. U.S. Pat. No. 4,883,750 (incorporated by reference herein in its entirety) describes a method similar to LCR for binding probe pairs to a target sequence.

Qbeta replicase (QβR), described in PCT Application No. PCT/US87/00880, (incorporated herein by reference), can also be used as an amplification method in the present invention. In this method, a replicative sequence of RNA that has a region complementary to that of a target is added to a sample in the presence of an RNA polymerase. The polymerase will copy the replicative sequence that can then be detected.

An isothermal amplification method, in which restriction endonucleases and ligases are used to achieve the amplification of target molecules that contain nucleotide 5′-[alpha-thio]triphosphates in one strand of a restriction site may also be useful in the amplification of nucleic acids in the present invention.

Strand Displacement Amplification (SDA), described in U.S. Pat. Nos. 5,455,166, 5,648,211, 5,712,124 and 5,744,311, each incorporated herein by reference, is another method of carrying out isothermal amplification of nucleic acids which involves multiple rounds of strand displacement and synthesis, i.e., nick translation. A similar method, called Repair Chain Reaction (RCR), involves annealing several probes throughout a region targeted for amplification, followed by a repair reaction in which only two of the four bases are present.

The other two bases can be added as biotinylated derivatives for easy detection. A similar approach is used in SDA. Target specific sequences can also be detected using a cyclic probe reaction (CPR). In CPR, a probe having 3′ and 5′ sequences of non-specific DNA and a middle sequence of specific RNA is hybridized to DNA that is present in a sample. Upon hybridization, the reaction is treated with RNase H, and the products of the probe identified as distinctive products that are released after digestion. The original template is annealed to another cycling probe and the reaction is repeated.

Still another amplification method, as described in Intl. Pat. Appl. No. PCT/US89/01025, which is incorporated herein by reference in its entirety, may be used in accordance with the present invention. In one embodiment, “modified” primers are used in a PCR-like, template- and enzyme-dependent synthesis. The primers may be modified by labeling with a capture moiety (e.g., biotin) and/or a detectable moiety (e.g., enzyme). In another embodiment, an excess of labeled probes is added to a sample. In the presence of the target sequence, the probe binds and is cleaved catalytically. After cleavage, the target sequence is released intact, available to be bound by excess probe. Cleavage of the labeled probe signals the presence of the target sequence.

Other nucleic acid amplification procedures include transcription-based amplification systems (TAS), including nucleic acid sequence based amplification (NASBA) and 3 SR (PCT Publication No. WO 88/10315, incorporated herein by reference). In NASBA, the nucleic acids can be prepared for amplification by standard phenol/chloroform extraction, heat denaturation of a clinical sample, treatment with lysis buffer and minispin columns for isolation of DNA and RNA or guanidinium chloride extraction of RNA. These amplification techniques involve annealing a primer that has target specific sequences. Following polymerization, DNA/RNA hybrids are digested with RNase H while double stranded DNA molecules are heat denatured again. In either case the single stranded DNA is made fully double stranded by addition of second target specific primer, followed by polymerization. The double-stranded DNA molecules are then multiply transcribed by an RNA polymerase such as T7, T3 or SP6. In an isothermal cyclic reaction, the RNAs are reverse transcribed into single stranded DNA, which is then converted to double-stranded DNA, and then transcribed once again with an RNA polymerase such as T7, T3 or SP6. The resulting products, whether truncated or complete, indicate target specific sequences.

European Pat. Appl. No. 329822 (incorporated herein by reference in its entirety) discloses a nucleic acid amplification process involving cyclically synthesizing single stranded RNA (ssRNA), ssDNA, and double-stranded DNA (dsDNA), which can be used in accordance with the present invention. The ssRNA is a template for a first primer oligonucleotide, which is elongated by reverse transcriptase (RNA-dependent. DNA polymerase). The RNA is then removed from the resulting DNA:RNA duplex by the action of ribonuclease H (RNase H, an RNase specific for RNA in duplex with either DNA or RNA).

The resultant ssDNA is a template for a second primer, which also includes the sequences of an RNA polymerase promoter (exemplified by T7 RNA polymerase) 5′ to its homology to the template. This primer is then extended by DNA polymerase (exemplified by the large Klenow fragment of E. coli DNA polymerase I), resulting in a double-stranded DNA (dsDNA) molecule, having a sequence identical to that of the original RNA between the primers and having additionally, at one end, a promoter sequence. This promoter sequence can be used by the appropriate RNA polymerase to make many RNA copies of the DNA. These copies can then re-enter the cycle, leading to very swift amplification. With proper choice of enzymes, this amplification can be done isothermally without addition of enzymes at each cycle. Because of the cyclical nature of this process, the starting sequence can be chosen to be in the form of either DNA or RNA.

PCT Application WO 89/06700 (incorporated herein by reference in its entirety) discloses a nucleic acid sequence amplification scheme based on the hybridization of a promoter/primer sequence to a target single-stranded DNA (ssDNA), followed by transcription of many RNA copies of the sequence. This scheme is not cyclic, i.e., new templates are not produced from the resultant RNA transcripts. Other amplification methods include “RACE” and “one-sided PCR” (Frohman, 1990, incorporated by reference herein).

Methods based on ligation of two (or more) oligonucleotides in the presence of nucleic acid having the sequence of the resulting “di-oligonucleotide,” thereby amplifying the dioligonucleotide, can also be used in the amplification step of the present invention.

Following any amplification, it is desirable to separate the amplification product from the template and the excess primer for the purpose of determining whether specific amplification has occurred. In one embodiment, amplification products can be separated by agarose, agarose-acrylamide or polyacrylamide gel electrophoresis using standard methods (e.g., Sambrook et al., 1989).

Alternatively, chromatographic techniques can be used to effect separation. There are many kinds of chromatography that can be used in the present invention: such as, for example, adsorption, partition, ion exchange and molecular sieve, as well as many specialized techniques for using them including column, paper, thin-layer and gas chromatography.

Amplification products must be visualized in order to confirm amplification of the target sequences. One typical visualization method involves staining of a gel with ethidium bromide and visualization under UV light. Alternatively, if the amplification products are integrally labeled with radio- or fluorometrically-labeled nucleotides, the amplification products can then be exposed to x-ray film or visualized under the appropriate stimulating spectra, following separation.

In some embodiments, visualization is achieved indirectly. Following separation of amplification products, a labeled, nucleic acid probe is brought into contact with the amplified target sequence. The probe preferably is conjugated to a chromophore but may be radiolabeled. In another embodiment, the probe is conjugated to a binding partner, such as an antibody or biotin, and the other member of the binding pair carries a detectable moiety.

In other embodiments, detection can be by Southern or Northern blotting and hybridization with a labeled probe. The techniques involved in Southern and Northern blotting are well known to those of skill in the art and can be found in many standard books on molecular protocols (e.g., Sambrook et al., 1989). Briefly, amplification products are separated by gel electrophoresis. The gel is then contacted with a membrane, such as nitrocellulose, permitting transfer of the nucleic acid and noncovalent binding. Subsequently, the membrane is incubated with a chromophore-conjugated probe that is capable of hybridizing with a target amplification product. Detection is by exposure of the membrane to x-ray film or ion-emitting detection devices. One example of the foregoing is described in U.S. Pat. No. 5,279,721, incorporated by reference herein, which discloses an apparatus and method for the automated electrophoresis and transfer of nucleic acids. The apparatus permits electrophoresis and blotting without external manipulation of the gel.

Additionally, a wide variety of labeling and conjugation techniques are known in the art that are used in various nucleic acid detection and amplification assays. Methods for producing labeled hybridization probes and/or PCR or other ligation primers for detecting and/or amplifying nucleic acid sequences can include, for example, oligolabeling, nick translation and end-labeling, as well as other well known methods. Alternatively, nucleic acid sequences encoding the polypeptides of this invention, and/or any functional fragment thereof, can be cloned into a plasmid or vector for detection and amplification. Such plasmids and vectors are well known in the art and are commercially available. It is also contemplated that the methods of this invention can be conducted using a variety of commercially available kits (e.g., Pharmacia & Upjohn; Promega; U.S. Biochemical Corp.). Suitable reporter molecules or labels, which can be used for ease of detection, include, for example, radionuclides, enzymes, fluorescence agents, chemiluminescence agents and chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles and the like as are well known in the art.

The present invention further includes isolated polypeptides, peptides, proteins, fragments, domains and/or nucleic acid molecules that are substantially equivalent to those described for this invention. As used herein, “substantially equivalent” can refer both to nucleic acid and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an undesirable adverse functional dissimilarity between reference and subject sequences. In some embodiments, this invention can include substantially equivalent sequences that have an adverse functional dissimilarity. For purposes of the present invention, sequences having equivalent biological activity and equivalent expression characteristics are considered substantially equivalent.

The invention further provides homologs, as well as methods of obtaining homologs, of the polypeptides and/or fragments of this invention. As used herein, an amino acid sequence or protein is defined as a homolog of a polypeptide or fragment of the present invention if it shares significant homology to one of the polypeptides and/or fragments of the present invention. Significant homology means at least 60%, 65%, 75%, 80%, 85%, 90%, 95%, 98% and/or 100% homology with another amino acid sequence. Specifically, by using the nucleic acids disclosed herein as a probe or as primers, and techniques such as PCR amplification and colony/plaque hybridization, one skilled in the art can identify homologs of the polypeptides and/or fragments of this invention.

In further embodiments, the nucleic acids encoding the polypeptides and/or fragments of this invention can be part of a recombinant nucleic acid construct comprising any combination of restriction sites and/or functional elements as are well known in the art that facilitate molecular cloning and other recombinant DNA manipulations. Thus, the present invention further provides a recombinant nucleic acid construct comprising a nucleic acid encoding a polypeptide and/or biologically active fragment of this invention.

The present invention further provides a vector comprising a nucleic acid encoding a polypeptide and/or fragment of this invention. The vector can be an expression vector which contains all of the genetic components required for expression of the nucleic acid in cells into which the vector has been introduced, as are well known in the art. The expression vector can be a commercial expression vector or it can be constructed in the laboratory according to standard molecular biology protocols. The expression vector can comprise viral nucleic acid including, but not limited to, poxvirus, vaccinia virus, adenovirus, retrovirus and/or adeno-associated virus nucleic acid. The nucleic acid or vector of this invention can also be in a liposome or a delivery vehicle, which can be taken up by a cell via receptor-mediated or other type of endocytosis.

The nucleic acid of this invention can be in a cell, which can be a cell expressing the nucleic acid whereby a polypeptide and/or biologically active fragment of this invention is produced in the cell. In addition, the vector of this invention can be in a cell, which can be a cell expressing the nucleic acid of the vector whereby a polypeptide and/or biologically active fragment of this invention is produced in the cell. It is also contemplated that the nucleic acids and/or vectors of this invention can be present in a host animal (e.g., a transgenic animal), which expresses the nucleic acids of this invention and produces the polypeptides and/or fragments of this invention.

The nucleic acid encoding the polypeptide and/or fragment of this invention can be any nucleic acid that functionally encodes the polypeptides and/or fragments of this invention. To functionally encode the polypeptides and/or fragments (i.e., allow the nucleic acids to be expressed), the nucleic acid of this invention can include, for example, expression control sequences, such as an origin of replication, a promoter, an enhancer and necessary information processing sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites and transcriptional terminator sequences.

Nonlimiting examples of expression control sequences that can be present in a nucleic acid of this invention include promoters derived from metallothionine genes, actin genes, immunoglobulin genes, CMV, SV40, adenovirus, bovine papilloma virus, etc. A nucleic acid encoding a selected polypeptide and/or fragment can readily be determined based upon the genetic code for the amino acid sequence of the selected polypeptide and/or fragment and many nucleic acids will encode any selected polypeptide and/or fragment. Modifications in the nucleic acid sequence encoding the polypeptide and/or fragment are also contemplated. Modifications that can be useful are modifications to the sequences controlling expression of the polypeptide and/or fragment to make production of the polypeptide and/or fragment inducible or repressible as controlled by the appropriate inducer or repressor. Such methods are standard in the art. The nucleic acid of this invention can be generated by means standard in the art, such as by recombinant nucleic acid techniques and/or by synthetic nucleic acid synthesis or in vitro enzymatic synthesis.

The nucleic acids and/or vectors of this invention can be transferred into a host cell (e.g., a prokaryotic or eukaryotic cell) by well-known methods, which vary depending on the type of cell host. For example, calcium chloride transfection is commonly used for prokaryotic cells, whereas calcium phosphate treatment, transduction and/or electroporation can be used for other cell hosts.

As used herein, “a” or “an” or “the” can mean one or more than one. For example, “a” cell can mean one cell or a plurality of cells.

Also as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).

Furthermore, the term “about,” as used herein when referring to a measurable value such as an amount of a compound or agent of this invention, dose, time, temperature, and the like, is meant to encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount.

A T cell of this invention includes but is not limited to CD4+ T cells, T regulatory cells, double positive (CD4+, CD8+) T cells and double negative (CD4−, CD8−) T cells. A B cell of this invention is, e.g., an antibody producing cell and can be for example, a plasma B cell, a memory B cell, a B-1 cell or a B-2 cell.

As used herein, “T cell activation” or “B cell activation” means a process or activity that causes T cells or B cells to exhibit a phenotype of an activated T cell or B cell, and “activated T cell” or “activated B cell” describes T cells or B cells that can exhibit some of the following phenotypes: T cell activation can be measured by methods not limited to the following: CD69, CD25, HLA-DR, CD62L and/or CD154 expression and/or the production of IL-2, calcium mobilization, ZAP-70 phosphorylation, LAT phosphorylation, Lck phosphorylation, NF-κB activation, MEK activation, NFAT activation, Ap-1 activation; T cell proliferation and cytotoxicity (defined as the ability to kill target cells). B cell activation can be measured by any methods known in the art to identify antigen-mediated activation, T cell dependent activation, T cell-independent activation, etc.

Nonlimiting examples of a Sema6D protein of this invention have an amino acid sequence as shown in the Sequence Listing. For example SEQ ID NOs: 22, 24, 26, 28, 30 and are examples of human isoforms of a Sema6D protein. Other Sema6D proteins as are known in the art and as described herein are also included in the present invention.

As used herein, “modulate,” “modulates” or “modulation” refers to enhancement (e.g., an increase) or inhibition (e.g., diminished, reduced or suppressed) of the specified activity. The term “enhancement,” “enhance,” “enhances,” or “enhancing” refers to an increase in the specified parameter (e.g., at least about a 1.1-fold, 1.25-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 8-fold, 10-fold, twelve-fold, or even fifteen-fold or more increase) and/or an increase in the specified activity of at least about 5%, 10%, 25%, 35%, 40%, 50%, 60%, 75%, 80%, 90%, 95%, 97%, 98%, 99% or 100%. The term “inhibit,” “diminish,” “reduce” or “suppress” refers to a decrease in the specified parameter (e.g., at least about a 1.1-fold, 1.25-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 8-fold, 10-fold, twelve-fold, or even fifteen-fold or more decrease) and/or a decrease or reduction in the specified activity of at least about 5%, 10%, 25%, 35%, 40%, 50%, 60%, 75%, 80%, 90%, 95%, 97%, 98%, 99% or 100%. In particular embodiments, the inhibition or reduction results in little or essentially no detectable activity (at most, an insignificant amount, e.g., less than about 10% or about 5%).

The term “overexpress,” “overexpresses” or “overexpression” as used herein in connection with isolated nucleic acids encoding Sema6D refers to expression that results in higher levels of Sema6D polypeptide than exist in the cell in its native (control) state. Overexpression of Sema6D can result in levels that are 25%, 50%, 100%, 200%, 500%, 1000%, 2000% or higher in the cell. Further, nucleic acid encoding Sema6D can be introduced into a cell that does not produce the specified form of Sema6D (e.g., an isoform) encoded by the transgene or does so only at negligible levels.

The term “enhance,” “enhances,” “enhancing” or “enhancement” with respect to T cell or B cell activation refers to an increase in T cell or B cell activation (e.g., at least about a 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 8-fold, 10-fold, twelve-fold, or even fifteen-fold or more increase), for example, in response to a substance that enhances T cell or B cell activation. Alternatively, these terms can refer to increasing expression of nucleic acid encoding Sema6D in a cell or subject in response to an enhancer as compared with the amount of Sema6D nucleic acid expression in the absence of the enhancer.

A “fusion polypeptide” is a polypeptide produced when two heterologous nucleotide sequences or fragments thereof coding for two (or more) different polypeptides not found fused together in nature are fused together in the correct translational reading frame. Illustrative fusion polypeptides include, but are not limited to a fusion of the extracellular domain of Sema6D or active fragment thereof to an immunoglobulin fragment as described herein. Ig fragments from human, mouse, rat, goat, rabbit can all be used. In addition, mutations in the Fc binding sequence do not alter the function of the protein, and these can also be used. When used in animals, it is best to use the IgG fusion that is from the same species. For example, using human IgG fusion protein to perform in mice may cause immunogenicity in the long run, although for short term experiments, this is less of a concern.

As used herein, a “functional” or “active” polypeptide is one that retains at least one biological activity normally associated with that polypeptide. Preferably, a “functional” polypeptide retains all of the activities possessed by the unmodified peptide. By “retains” biological activity, it is meant that the polypeptide retains at least about 50%, 60%, 75%, 85%, 90%, 95%, 97%, 98%, 99%, or more, of the biological activity of the native polypeptide (and can even have a higher level of activity than the native polypeptide). A “non-functional” polypeptide is one that exhibits essentially no detectable biological activity normally associated with the polypeptide (e.g., at most, only an insignificant amount, e.g., less than about 10% or even 5%).

As used herein, the transitional phrase “consisting essentially of” means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim, “and those that do not materially affect the basic and novel characteristic(s)” of the claimed invention. See, In re Herz, 537 F.2d 549, 551-52, 190 USPQ 461, 463 (CCPA 1976) (emphasis in the original); see also MPEP §2111.03. Thus, the term “consisting essentially of” when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”

“Isolated” as used herein means the nucleic acid or protein or protein fragment of this invention is sufficiently free of contaminants or cell components with which nucleic acids or proteins normally occur. “Isolated” does not mean that the preparation is technically pure (homogeneous), but it is sufficiently pure to provide the nucleic acid or protein or protein fragment in a form in which it can be used therapeutically.

“Epitope” or “antigenic epitope” or “antigenic peptide” as used herein means a specific amino acid sequence which, when present in the proper conformation, provides a reactive site for an antibody or T cell receptor. The identification of epitopes on antigens can be carried out by immunology protocols that are well known in the art. Typically, an epitope or antigenic peptide can be 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45 or 50 amino acids in length.

As used herein, the term “polypeptide” or “protein” is used to describe a chain of amino acids that correspond to those encoded by a nucleic acid. A polypeptide of this invention can be a peptide, which usually describes a chain of amino acids of from two to about 30 amino acids. The term polypeptide as used herein also describes a chain of amino acids having more than 30 amino acids and can be a fragment or domain of a protein or a full length protein. Furthermore, as used herein, the term polypeptide can refer to a linear chain of amino acids or it can refer to a chain of amino acids that has been processed and folded into a functional protein. It is understood, however, that 30 is an arbitrary number with regard to distinguishing peptides and polypeptides and the terms can be used interchangeably for a chain of amino acids. The polypeptides of the present invention are obtained by isolation and purification of the polypeptides from cells where they are produced naturally, by enzymatic (e.g., proteolytic) cleavage, and/or recombinantly by expression of nucleic acid encoding the polypeptides or fragments of this invention. The polypeptides and/or fragments of this invention can also be obtained by chemical synthesis or other known protocols for producing polypeptides and fragments.

The amino acid sequences disclosed herein are presented in the amino to carboxy direction, from left to right. Nucleotide sequences are presented herein in the 5′ to 3′ direction, from left to right. It is intended that the nucleic acids of this invention can be either single or double stranded (i.e., including the complementary nucleic acid). A nucleic acid of this invention can be the complement of a nucleic acid described herein.

A “biologically active fragment” or “active fragment” or “functional fragment” or “functionally active fragment” as used herein includes a polypeptide of this invention that comprises a sufficient number of amino acids to have one or more of the biological activities of the polypeptides of this invention. Such biological activities can include, but are not limited to, in any combination, binding activity, immunomodulating activity and/or immunogenic activity, as well as any other activity now known or later identified for the polypeptides and/or fragments of this invention. A fragment of a polypeptide of this invention can be produced by methods well known and routine in the art. Fragments of this invention can be produced, for example, by enzymatic or other cleavage of naturally occurring peptides or polypeptides or by synthetic protocols that are well known. Such fragments can be tested for one or more of the biological activities of this invention according to the methods described herein, which are routine methods for testing activities of polypeptides, and/or according to any art-known and routine methods for identifying such activities. Such production and testing to identify biologically active fragments of the polypeptides described herein would be well within the scope of one of ordinary skill in the art and would be routine.

Fragments of the polypeptides of this invention are preferably at least about ten amino acids in length and retain one or more of the biological activities (e.g., immunomodulating; binding) and/or the immunological activities of the proteins of this invention. Examples of the fragments of this invention include, but are not intended to be limited to, the following fragments identified by the amino acid number as shown in the Sequence Listing herein: Amino acids 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 110-120, 120-130, 130-140, 140-150, 150-160, 160-170, 170-180, 180-190, 190-200, 200-210, 210-220, 220-230, 230-240, 240-250, 1-25, 1-50, 1-67, 1-75, 1-100, 1-125, 1-135, 1-145, 1-150, 1-160, 1-170, 1-180, 1-190, 1-200, 1-250, 68-180, 183-223, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-650, etc.

It is understood that this list is exemplary only and that a fragment of this invention can be any amino acid sequence containing any combination of contiguous amino acids that are numbered in the Sequence Listing as amino acids 1 through 652. even if that combination is not specifically recited as an example herein. It is also understood that these fragments can be combined in any order or amount. For example, fragment 1-10 can be combined with fragment 10-20 to produce a fragment of amino acids 1-20. As another example, fragment 1-20 can be combined with fragment 50-60 to produce a single fragment of this invention having 31 amino acids (AA 10-20 and AA 50-60). Also fragments can be present in multiple numbers and in any combination in a fragment of this invention. Thus, for example, fragment 1-150 can be combined with a second fragment 1-150 and/or combined with fragment 400-500 to produce a fragment of this invention.

The terms “homology,” “identity” and “complementarity” as used herein refer to a degree of similarity between two or more sequences. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to as “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence can be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or hybridization probe will compete for and inhibit the binding of a completely homologous sequence to the target sequence under conditions of low stringency, as this term is known in the art. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding can be tested by the use of a second target sequence that lacks even a partial degree of complementarity (e.g., less than about 30% identity). In the absence of non-specific binding, the probe will not hybridize to the second non-complementary target sequence.

The term “hybridization” as used herein refers to any process by which a first strand of nucleic acid binds with a second strand of nucleic acid through base pairing. Nucleic acids encoding the polypeptides and/or fragments of this invention can be detected by DNA-DNA or DNA-RNA hybridization and/or amplification using probes, primers and/or fragments of polynucleotides encoding the polypeptides and/or fragments of this invention and/or designed to detect and/or amplify the nucleic acids of this invention.

The term “hybridization complex” as used herein refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary G and C bases and between complementary A and T bases; these hydrogen bonds may be further stabilized by base stacking interactions. The two complementary nucleic acid sequences hydrogen bond in an antiparallel configuration. A hybridization complex may be formed in solution (e.g., C₀t or R₀t analysis) or between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells and/or nucleic acids have been fixed).

The term “nucleotide sequence” refers to a heteropolymer of nucleotides or the sequence of these nucleotides. The terms “nucleic acid,” “oligonucleotide” and “polynucleotide” are also used interchangeably herein to refer to a heteropolymer of nucleotides. Generally, nucleic acid segments provided by this invention may be assembled from fragments of the genome and short oligonucleotide linkers, or from a series of oligonucleotides, or from individual nucleotides, to provide a synthetic nucleic acid which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon, or a eukaryotic gene. Nucleic acids of this invention can comprise a nucleotide sequence that can be identical in sequence to the sequence which is naturally occurring or, due to the well-characterized degeneracy of the nucleic acid code, can include alternative codons that encode the same amino acid as that which is found in the naturally occurring sequence. Furthermore, nucleic acids of this invention can comprise nucleotide sequences that can include codons which represent conservative substitutions of amino acids as are well known in the art, such that the biological activity of the resulting polypeptide and/or fragment is retained.

The term “probe” or “primer” includes naturally occurring and/or recombinant and/or chemically synthesized single- and/or double-stranded nucleic acids. They can be labeled for detection by nick translation, Klenow fill-in reaction, PCR and/or other methods well known in the art. Probes and primers of the present invention, their preparation and/or labeling are described in Sambrook et al. 1989. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY and Ausubel et al. 1989. Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., both of which are incorporated herein by reference in their entirety for these teachings.

The term “stringent” as used herein refers to hybridization conditions that are commonly understood in the art to define the conditions of the hybridization procedure. Stringency conditions can be low, high or medium, as those terms are commonly know in the art and well recognized by one of ordinary skill. In various embodiments, stringent conditions can include, for example, highly stringent (i.e., high stringency) conditions (e.g., hybridization in 0.5 M NaHPO₄, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at about 68° C.), and/or moderately stringent (i.e., medium stringency) conditions (e.g., washing in 0.2×SSC/0.1% SDS at about 42° C.).

“Amplification” as used herein includes the production of multiple copies of a nucleic acid molecule and is generally carried out using polymerase chain reaction (PCR) and/or any other amplification technologies as are well known in the art (Dieffenbach and Dveksler. 1995. PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.).

“Effective amount” as used herein refers to an amount of a compound, agent, substance or composition of this invention that is sufficient to produce a desired effect, which can be a therapeutic effect. The effective amount will vary with the age, general condition of the subject, the severity of the condition being treated, the particular compound, agent, substance or composition administered, the duration of the treatment, the nature of any concurrent treatment, the pharmaceutically acceptable carrier used if any, and like factors within the knowledge and expertise of those skilled in the art. As appropriate, an “effective amount” in any individual case can be determined by one of ordinary skill in the art by reference to the pertinent texts and literature and/or by using routine experimentation. (Remington, The Science And Practice of Pharmacy (20th ed. 2000)).

A “pharmaceutically acceptable” component such as a salt, carrier, excipient or diluent of a composition according to the present invention is a component that (i) is compatible with the other ingredients of the composition in that it can be combined with the compositions of the present invention without rendering the composition unsuitable for its intended purpose, and (ii) is suitable for use with subjects as provided herein without undue adverse side effects (such as toxicity, irritation, and allergic response). Side effects are “undue” when their risk outweighs the benefit provided by the composition. Non-limiting examples of pharmaceutically acceptable components (e.g., pharmaceutically acceptable carriers) include any of the standard pharmaceutical carriers such as phosphate buffered saline solutions, water, emulsions such as oil/water emulsion, microemulsions and various types of wetting agents. In particular, it is intended that a pharmaceutically acceptable carrier be a sterile carrier that is formulated for administration to or delivery into a subject of this invention.

The compositions of the present invention can also include other medicinal agents, pharmaceutical agents, carriers, diluents, immunostimulatory cytokines, etc. and can be in a pharmaceutically acceptable carrier. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art.

An “immunomodulatory molecule” of this invention can be, but is not limited to an immunostimulatory cytokine that can be, but is not limited to, GM/CSF, interleukin-2, interleukin-12, interferon-gamma, interleukin-4, tumor necrosis factor-alpha, interleukin-1, hematopoietic factor flt3L, CD40L, B7.1 co-stimulatory molecules and B7.2 co-stimulatory molecules.

Additional examples of an immunomodulatory molecule of this invention include the adjuvants of this invention, including, for example, SYNTEX adjuvant formulation 1 (SAF-1) composed of 5 percent (wt/vol) squalene (DASF, Parsippany, N.J.), 2.5 percent Pluronic, L121 polymer (Aldrich Chemical, Milwaukee), and 0.2 percent polysorbate (Tween 80, Sigma) in phosphate-buffered saline. Suitable adjuvants also include an aluminum salt such as aluminum hydroxide gel (alum), aluminum phosphate, or algannmulin, but may also be a salt of calcium, iron or zinc, or may be an insoluble suspension of acylated tyrosine, or acylated sugars, cationically or anionically derivatized polysaccharides, or polyphosphazenes.

Other adjuvants are well known in the art and include QS-21, Freund's adjuvant (complete and incomplete), aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE) and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trealose dimycolate and cell wall skeleton (MPL+TDM+CWS) in 2% squalene/Tween 80 emulsion.

Additional adjuvants can include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl. lipid A (3D-MPL) together with an aluminum salt. An enhanced adjuvant system involves the combination of a monophosphoryl lipid A and a saponin derivative, particularly the combination of QS21 and 3D-MPL as disclosed in PCT publication number WO 94/00153 (the entire contents of which are incorporated herein by reference), or a less reactogenic composition where the QS21 is quenched with cholesterol as disclosed in PCT publication number WO 96/33739 (the entire contents of which are incorporated herein by reference). A particularly potent adjuvant formulation involving QS21 3D-MPL & tocopherol in an oil in water emulsion is described in PCT publication number WO 95/17210 (the entire contents of which are incorporated herein by reference). In addition, the nucleic acid of this invention can include an adjuvant by comprising a nucleotide sequence encoding a Sema6D protein or active fragment thereof of this invention and a nucleotide sequence that provides an adjuvant function, such as CpG sequences. Such CpG sequences, or motifs, are well known in the art. Other TLR agonists, such as Pam3Cys, Poly(I:C), single stranded RNA, as well as CATERPILLER (NOD-LRR) agonists, such as proteoglycan-derived products, are also included herein.

The terms “treat,” “treating” or “treatment” include any type of action that imparts a modulating effect, which, for example, can be a beneficial effect, to a subject afflicted with a disorder, disease, condition or illness, including improvement in the disorder, disease, condition or illness of the subject (e.g., in one or more symptoms), delay in the progression of the disorder, disease, condition or illness, prevention or delay of the onset of the disorder, disease, condition or illness, and/or change in clinical parameters, disorder, disease, condition or illness status, etc., as would be well known in the art.

As used herein, the term “antibody” includes intact immunoglobulin molecules as well as fragments thereof that are capable of binding the epitopic determinant of an antigen (i.e., antigenic determinant). Antibodies that bind the polypeptides of this invention are prepared using intact polypeptides or fragments as the immunizing antigen. The polypeptide or fragment used to immunize an animal can be derived from enzymatic cleavage, recombinant expression, isolation from biological materials, synthesis, etc., and can be conjugated to a carrier protein, if desired. Commonly used carriers that are chemically coupled to peptides and proteins for the production of antibody include, but are not limited to, bovine serum albumin, thyroglobulin and keyhole limpet hemocyanin. The coupled peptide or protein is then used to immunize the animal (e.g., a mouse, rat, or rabbit). The polypeptide or peptide antigens can also be administered with an adjuvant, as described herein and as otherwise known in the art.

An antibody of this invention can be any type of immunoglobulin, including IgG, IgM, IgA, IgD, and/or IgE. The antibody can be monoclonal or polyclonal and can be of any species of origin, including, for example, mouse, rat, rabbit, horse, goat, sheep or human, or can be a chimeric or humanized antibody (e.g., Walker et al., Molec. Immunol. 26:403-11 (1989)). The antibodies can be recombinant monoclonal antibodies produced according to the methods disclosed in U.S. Pat. No. 4,474,893 or U.S. Pat. No. 4,816,567. The antibodies can also be chemically constructed according to methods disclosed in U.S. Pat. No. 4,676,980. The antibody can further be a single chain antibody (e.g., scFv) or bispecific antibody.

Antibody fragments included within the scope of the present invention include, for example, Fab, F(ab′)2, and Fc fragments, and the corresponding fragments obtained from antibodies other than IgG. Such fragments can be produced by known techniques. For example, F(ab′)2 fragments can be produced by pepsin digestion of the antibody molecule, and Fab fragments can be generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries can be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse et al., (1989) Science 254:1275-1281). Antibodies can also be obtained by phage display techniques known in the art or by immunizing a heterologous host with a cell containing an epitope of interest.

The polypeptide, fragment or antigenic epitope that is used as an immunogen can be modified or administered in an adjuvant in order to increase antigenicity. Methods of increasing the antigenicity of a protein or peptide are well known in the art and include, but are not limited to, coupling the antigen with a heterologous protein (such as globulin or β-galactosidase) or through the inclusion of an adjuvant during immunization.

For example, for the production of antibodies, various hosts including goats, rabbits, rats, mice, humans, and others, can be immunized by injection with the polypeptides and/or fragments of this invention, with or without a carrier protein. Additionally, various adjuvants may be used to increase the immunological response. Such adjuvants include, but are not limited to, Freund's complete and incomplete adjuvants, mineral gels such as aluminum hydroxide, and surface-active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are especially preferable.

Monoclonal antibodies can be produced in a hybridoma cell line according to the technique of Kohler and Milstein (Nature 265:495-97 (1975)). Other techniques for the production of monoclonal antibodies include, but are not limited to, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kozbor et al. 1985. J. Immunol. Methods 81:31-42; Cote et al. 1983. Proc. Natl. Acad. Sci. 80:2026-2030; Cole et al. 1984. Mol. Cell Biol. 62:109-120).

For example, to produce monoclonal antibodies, a solution containing the appropriate antigen can be injected into a mouse and, after a sufficient time, the mouse sacrificed and spleen cells obtained. The spleen cells are then immortalized by fusing them with myeloma cells or with lymphoma cells, typically in the presence of polyethylene glycol, to produce hybridoma cells. The hybridoma cells are then grown in a suitable medium and the supernatant screened for monoclonal antibodies having the desired specificity. Monoclonal Fab fragments can be produced in a bacterial cell such as E. coli by recombinant techniques known to those skilled in the art (e.g., Huse. Science 246:1275-81 (1989)). Any one of a number of methods well known in the art can be used to identify the hybridoma cell, which produces an antibody with the desired characteristics. These include screening the hybridomas by ELISA assay, Western blot analysis, or radioimmunoassay. Hybridomas secreting the desired antibodies are cloned and the class and subclass are identified using standard procedures known in the art.

For polyclonal antibodies, antibody-containing serum is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using any of the well known procedures as described herein.

The present invention further provides antibodies of this invention in detectably labeled form. Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, etc.) fluorescence labels (such as FITC or rhodamine, etc.), paramagnetic atoms, gold beads, etc. Such labeling procedures are well-known in the art. The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify a polypeptide and/or fragment of this invention in a sample.

In some embodiments, the present invention further provides the above-described antibodies immobilized on a solid support (e.g., beads, plates, slides or wells formed from materials such as latex or polystyrene). Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir et al., Handbook of Experimental Immunology 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986)). Antibodies can likewise be conjugated to detectable groups such as radiolabels (e.g., ³⁵S, ¹²⁵I, ¹³¹I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescence labels (e.g., fluorescein) in accordance with known techniques. Determination of the formation of an antibody/antigen complex in the methods of this invention can be by detection of, for example, precipitation, agglutination, flocculation, radioactivity, color development or change, fluorescence, luminescence, etc., as is well know in the art.

In addition, techniques developed for the production of chimeric antibodies or humanized antibodies by splicing mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity can be used (Morrison et al. 1984. Proc. Natl. Acad. Sci. 81:6851-6855; Neuberger et al. 1984. Nature 312:604-608; Takeda et al. 1985. Nature 314:452-454). Alternatively, techniques described for the production of single chain antibodies can be adapted, using methods known in the art, to produce single chain antibodies specific for the polypeptides and fragments of this invention. Antibodies with related specificity, but of distinct idiotypic composition, can be generated by chain shuffling from random combinatorial immunoglobulin libraries (Burton 1991. Proc. Natl. Acad. Sci. 88:11120-3).

Various immunoassays can be used for screening to identify antibodies having the desired specificity for the proteins and peptides of this invention. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificity are well known in the art. Such immunoassays typically involve the measurement of complex formation between an antigen and its specific antibody (e.g., antigen/antibody complex formation). For example, a two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on the proteins or peptides of this invention can be used, as well as a competitive binding assay.

The present invention is more particularly described in the following examples, which are intended as illustrative only since numerous modifications and variations therein will be apparent to those skilled in the art.

EXAMPLES I. The Semaphorin 6D Receptor on T Cells is Required for Activation of CD4⁺ T Cells

Mice.

All experiments were performed with 8-12 week old C57BL/6 mice from Jackson Labs. OT-II mice which express the OVA[323-339]-specific TCR transgene on the C57BL/6 background were generous gifts from M. Croft. All animal procedures were conducted in complete compliance with the NIH Guide for the Care and Use of Laboratory Animals, approved by the Institutional Animal Care and Use Committee of the University of North Carolina, Chapel Hill.

Cells.

Murine bone marrow derived dendritic cells (BMDCs) were isolated from bone marrow and grown in vitro for maturation. Briefly cells were grown in GM-CSF and IL-4 for 10 days before maturing with 20 ng/ml TNF-α for 2 additional days.

Magnetic Bead Isolation of TCR Tg OTII T Cells.

Splenic T cells were isolated from OTII mice based on expression of CD4. Magnetic bead purifications were performed according to the protocol provided by Miltenyi Biotec (Auburn, Calif.). Briefly, splenocytes isolated from B6 or OTII mice were incubated with anti-mouse CD4 antibody conjugated with PE (BD PharMingen, San Diego, Calif.). Spleen cell samples were then incubated with anti-PE antibody coated magnetic beads (Miltenyi Biotec, Auburn, Calif.) and cells positively selected by passage through LS columns attached to magnetic separators. Flow through and eluent fractions were collected following Miltenyi protocol guidelines.

SYBR Green Real-Time PCR.

SYBR Green qPCR Rox mix (Abgene) was used for all quantitative PCR experiments. The following cycle conditions were used: Stage 1) 50°, for 2 minutes; Stage 2) 95°, for 15 minutes; Stage 3) 95° for 15 seconds, 56-57° for 15-30 seconds, 72° for 15-30 seconds, repeat 40×; Stage 4) dissociation curve. The relative level of expression for each primer target was calculated via (ΔΔCT)×1000. Target genes were calculated in reference to β-actin for each sample. The β-actin primers used were: (Forward) 5′-agggctatgctctccctcac-3′ (SEQ ID NO:3) and (Reverse) 5′-ctctcagctgtggtggtgaa-3′ (SEQ ID NO:4). The Sema6D primers used were: (Forward) 5′-cagaagcatgggagatggat-3′ (SEQ ID NO:5) and (Reverse) 5′-gccacccatgtcgtttttac-3′ (SEQ ID NO:6).

Cloning and Production of Mouse Semaphorin 6D-Ig Fusion Protein (Sema6D-Ig).

Sema6D cDNA was obtained via reverse transcription reaction, according to manufacturer's instruction, utilizing Superscript III (Invitrogen) and an RNA sample isolated from the brain of C57BL/6J mice. Sema6D has multiple isoforms that differ slightly in the extracellular region between the Sema domain and the trans-membrane domain. Thus, to obtain a full length cDNA of Sema6D, the forward primer (5′-atggggttcettctgattggtt) (SEQ ID NO:7) and reverse primer (3′-ctagtacgtgtacttgttcagtggtctg) (SEQ ID NO:8) were designed utilizing current mRNA sequence for Sema6D contained within the GenBank database. PCR utilizing heat-stable DNA polymerase LATaq (TAKARA) followed by 0.8% agarose gel electrophoresis, produced a band of approximately 3 kb. The 3 kb DNA band was isolated and cloned into the pCR2.1 TOPO vector (Invitrogen). Multiple sequencing reactions (UNC-CH genomics core facility) verified that the cloned DNA sequence was identical to the full-length sequence of Sema6D isoform 6 (Sema6D-6).

Isolation of a cDNA fragment encoding the extracellular region of mouse Sema6D-6 (amino acids 1-652) was obtained via PCR amplification utilizing the full length Sema6D-6 cloned into the pCR2.1 TOPO vector. The forward primer (5′-gcggatatcgccacccatggggttccttctgattggttct) (SEQ ID NO:9) was designed to include a HindIII restriction endonuclease and the reverse primer (5′-gcgggatccagcggcaaacacgcaggtgatgagga) (SEQ ID NO:10) was designed with a BamHI restriction endonuclease site. The PCR product was gel purified and digested by HindIII and BamHI restriction endonucleases (New England Biolabs). The digested fragment containing most of the extracellular region of Sema6D (Sema6DEC) was subcloned into a modified pcDNA3.1 vector (Invitrogen) containing a human IgG1 fragment (Hinge-CH2-CH3). For transient expression, the sequenced SEMA6DEC-Ig plasmid was transfected into the COS-7 cell line (ATCC CRL-1651) via a standard calcium phosphate transfection protocol. Serum containing DMEM medium was substituted with a serum-free DMEM medium at 48 hour post transfection. The supernatant containing SEMA6DEC-Ig protein was harvested at 48-72 hours after transfection and purified by protein A affinity chromatography. Expression and secretion of SEMA6DEC-Ig was verified by immunoprecipitation followed by western blot analysis. Five milliliters of the supernatant were removed from Sema6DEC-Ig-transfected COS-7 cells cultured in serum-free DMEM 48 hours post transfection, and incubated with protein A/G agarose beads (Promega). Subsequent western blotting using anti-human IgG-HRP indicated a clear band of approximately 100 kDa and no other major bands that might represent either degradation products or contaminating proteins.

Generation of stable expression cells was performed via co-transfection of SEMA6DEC-Ig plasmid and a mouse dihydrofolate reductase (DHFR) encoding expression vector pSV2-dhfr (ATCC 37146) into DHFR-Chinese hamster ovary cells (CHO/DG44, Invitrogen) at a 20:1 ratio (weight:weight) through electroporation technique (300V, 960 uF, Bio-rad). Stable Sema6D-Ig expressing CHO cell clones were selected in Excell 302 serum free CHO medium (JRH Biosciences) supplemented with L-glutamine (Invitrogen) and 100 nM methotrexate (MTX, Sigma). Sema6D-Ig produced by the CHO cells was harvested from large-scale cultures via protein A affinity chromatography followed by gel filtration chromatography purification (Biosilect 400, Bio-rad).

Semi-Quantitative RT-PCR of Type III Semaphorin Transcripts.

Total RNA was isolated from DO11.10 T cells with or without activation, 3B11 cells at day 0, day 3, day 5 and day 7 of maturation, and brain cells using TRIzol Reagent (Invitrogen). One microgram of RNA of each sample was reverse transcribed using MMLV reverse transcriptase (Invitrogen). Semaphorin 3A, 3B, 3C, 3D and 3E transcripts were assessed using Taq polymerase (Invitrogen) and semi-quantitative PCR (22 cycles). Standardization of cDNA amounts was analyzed via PCR for 18S RNA. Sequences of the primers for the class III semaphorins are as follows: Semaphorin 3A, (forward) 5′-CGGGACTTCGCTATCTTCAG-3′ (SEQ ID NO:11) and (reverse) 5′-AGCATGAGTGGCTTTTCCAG-3′ (SEQ ID NO:12); Semaphorin 3B, (forward) 5′-GCTGTCTTCTCCACCTCCAG-3′ (SEQ ID NO:13) and (reverse) 5′-GGTTCCGACCAAACTGGATA-3 (SEQ ID NO:14)′; Semaphorin 3C, (forward) 5′-TCGGCAGTGTGTGTGTATCA-3′ (SEQ ID NO:15) and (reverse) 5′-CCTTCTGTGGATGGGGTAGA-3′ (SEQ ID NO:16); Semaphorin 3D, (forward) 5′-ATGGCTGATATCCGAGCAGT-3′ (SEQ ID NO:17) and (reverse) 5′-TTCTCTTGAAGGTCGGTGCT-3′ (SEQ ID NO:18); and Semaphorin 3E, (forward) 5′-GAGGCCATGCTGTATGTGTG-3′ (SEQ ID NO:19) and (reverse) 5′-CGTCATCGGGTAATCTTTGG-3′ (SEQ ID NO:20).

Flow Cytometry.

Following splenic or BM isolation, cells were suspended in ammonium chloride-Tris buffer (ACT) for 3 minutes at 37° C. to remove RBC. ACT treatment was performed with carboxyfluorescein diacetate succinimidyl ester (CFDAse, Molecular Probes, Eugene, Oreg.) labeled cells. Following ACT treatment, cells were washed and resuspended in 5% BCS in BSS and stained with the appropriate antibodies as described. For all studies, non-specific staining was reduced by addition of FcR blocking antibody and unlabeled Rat/Hamster Ig. Incubation with biotinylated antibodies was followed by incubation with Streptavidin-PE, PerCP or APC (BD PharMingen, San Diego, Calif.). Primary antibody incubations were for a minimum of 30 minutes at 4° C. followed by washing in BCS/BSS. Secondary antibody incubations were for a maximum of 15 minutes at 4° C. followed by washing in BCS/BSS. Stained cells were either analyzed immediately or fixed with 1% formaldehyde in 1.25×PBS. Staining was quantified with a Becton Dickinson FACSCalibur. A minimum of 50,000 events was collected and fluorescence signals detected via four-decade logarithmic amplification except for FSC and SSC which were detected via a linear scale. Spectral overlap compensation was made with single-color stained samples for each detection channel. For each experiment, data were analyzed using FlowJo software (Treestar, Calif.).

In Vitro CD3/CD28 Stimulation.

For stimulation of T cells, 5 μg/ml of anti-mouse CD3 and anti-mouse CD28 were added in PBS to cell culture plates for overnight coating at 4° C. For a 6 well plate, 1 ml/well was used. Following the overnight incubation, the plates were washed 3× with PBS or complete medium (cRPMI: RPMI+serum). Primary T cells isolated from spleens were incubated at 1×10⁶ cells/ml in 2 mls per well of a 6 well coated plate.

Ovalbumin (OVA) (Whole Protein or Peptide) Loading of DCs.

BMDCs, cultured for up to 10 days in cRPMI supplemented with GMCSF and IL4, were resuspended at a concentration of 1×10⁶ cells in 1 ml of cRPMI with 10 μg/mL whole OVA protein or peptide. The cells were incubated for 12 hrs at 37° C. with rotation. Following the incubation, the cells were washed 2× in cRPMI.

Adoptive Transfer.

Following isolation of splenocytes or BMDCs from mice, RBCs were lysed via incubation with ACT. The percentage of Tg OTII T cells within a population was determined by staining 2×10⁵ cells with anti-Vα2 and anti-Vβ5 in 5% BCS in BSS at 4° C. and analyzed via a Becton Dickinson FACSCalibur cell sorter. For each primary transfer, 3×10⁶ T cells and BMDCs were injected via tail vein into B6 recipient mice. Typically, three mice were used per experimental group.

CFSE Labeling of T Cells.

T cells labeled with carboxyfluorescein diacetate succinimidyl ester (CFDAse or CFSE; Molecular Probes, Eugene, Oreg.) were incubated at 37° C. for 10 minutes in serum free RPMI. The final concentration of CFSE used was 15 μM in RPMI with 10-20 million cells per ml. Following incubation with CFSE, the T cells were washed in cRPMI. Experimental conditions permitting, cells utilized for CFSE labeling were not treated with ASC red blood cell lysis buffer at the time of isolation.

Activation of T Cells by Co-Culture with Ag-Loaded BMDCs.

For in vitro activation, OTII TCR Tg (OVA-specific) T cells were incubated with immature BMDCs at a ratio of 1:1 in RPMI. OTII T cells were isolated from the spleens of Tg mice and purified by negative selection with T enrichment columns (R&D systems). Isolated T cells were labeled with CFSE or unlabeled prior to culture. BMDCs were either unloaded or loaded with OVA antigen (Ag) prior to culture. Approximately 0.5×10⁶ T cells and BMDCs were cultured in 1 ml per well of a 24 well plate. At the culture initiation, IL4 & GM-CSF were added at a concentration of 5 ηg/mL.

Use of Anti-Sema6D Antibody or the Sema6D-Ig Fusion Protein to Block the Functional Activation of T Cells.

Antibodies for blocking interactions between the T cells and BMDCs, such as anti-Sema6D Ab, were used at a final concentration of 10 μg/ml. The Sema6D-Ig fusion protein was used at a final concentration of 5 μg/ml. One day following initiation, cell cultures were supplemented with 1 ml of cRPMI. The cultured cells were analyzed by flow cytometry for indications of T cell activation via proliferation and expression of activation markers as described herein.

Activated CD4⁺ T Cells Express Semaphorin 6D In Vitro.

CD4⁺ T cells were isolated from splenocytes by magnetic bead separation and activated in vitro by anti-CD3 and anti-CD28 stimulation. Splenic CD4⁺ T cells were isolated by magnetic bead selection to a purity of greater than 90%. Purified T cells were cultured with plate bound anti-CD3 and -CD28 antibodies for stimulation. RNA was isolated from cultures at 12, 24 and 48 hr post initiation and analyzed by qPCR for Semaphorin 6D (Sema6D) expression. Following 12 hrs of stimulation, expression of Sema6D mRNA was increased as measured by qPCR, and this enhancement continued until at least 48 hrs post activation. Protein expression of Sema6D on activated CD4⁺ T cells was also examined by flow cytometry. Following 96 hrs of anti-CD3 and anti-CD28 stimulation, enhanced expression of CD25 and CD44 was detected on CD3⁺CD4⁺ T cells, indicative of their activation. Concurrently, upregulation of Sema6D was observed on CD3⁺CD4⁺ T cells following 96 hrs of stimulation. Isotype-matched control Ig showed no such increase. Thus, activation of CD4⁺ T cells via stimulation of CD3 and CD28 results in an upregulated expression of Sema6D at the cell surface. In contrast, measurements of Semaphorin 3A to 3F by the highly sensitive RT-PCR failed to detect any signals in resting or activated T cells. Semi-quantitative RT-PCR analysis revealed that OTII T cells did not express detectable levels of any type 3 semaphorins, including Sema 3A-E. Semaphorin 3 expression was detected in brain samples, used as positive controls.

DC Mediated Activation of Tg OTII T Cells Results in Sema6D Expression In Vivo.

Although expression of Sema6D in vitro via anti-CD3 and -CD28 stimulation was observed, it remained uncertain whether this result reflected the physiological reality of in vivo T cell activation. To examine the in vivo situation, the TCR transgenic (Tg) mouse line, OTII, whose CD4⁺ T cells express a TCR specific for the OVA antigen, was used. OTII Tg T cells were isolated from splenocytes and adoptively transferred to recipient mice with either OVA-loaded DCs (immune) or un-loaded DCs (naïve). The recipient mouse splenocytes were harvested at days 2, 3 and 4 post adoptive transfer and the cells were analyzed by flow cytometry. The activation and expansion of the OTII T cells were visualized as an expansion of the population of T cells expressing the Tg TCR Vα2 and Vβ5 chains. Proliferation of the OTII T cells was observed in vivo by day 2 and peaked at day 4, representing an approximately 5-fold expansion in immune vs. naïve mice. Concurrently, on day 4, the expression of CD25 was upregulated on OTII T cells from immune mice vs. naïve mice. This was accompanied by an upregulation of Sema6D on activated OTII T cells in vivo vs. naïve mice. Thus, in a physiologically relevant system of in vivo antigen presenting cell mediated T stimulation, enhanced expression of Sema6D on activated CD4⁺ T cells was observed, confirming the induction of Sema6D during T cell activation.

Blocking Sema6D Antibody Inhibits DC Mediated OTII T Cell Proliferation and Activation.

To examine the functional consequence of Sema6D expression on T cells, an in vitro DC-mediated T cell activation assay was used. Tg OTII T cells were cultured with OVA loaded BMDCs (OVA-BMDC) or unloaded BMDCs (BMDC). Following isolation but prior to co-culture, the OTII T cells were labeled with CFSE to enable monitoring of activation-induced proliferation. At days 2, 6 and 7 post culture initiation, cultured cells were collected and analyzed by flow cytometry. Activation is associated with proliferation, which results in a serial dilution of CFSE staining intensity with each cell division. Thus a pattern of serially diluted CFSE staining is indicative of T cell activation. OTII T cells cultured control exhibited little change, while OTII T cells incubated with OVA-BMDC cells displayed activation-induced proliferation as measured by a dilution of CFSE intensity. Initially, a small amount of proliferation was observed on day 2 post-culture of Vβ5⁺ (OTII) T cells with OVA-BMDC but not control BMDC (0.94% Vβ5⁺CFSE^(low) vs. 0.064%). By day 7 of co-culture, the OTII T cells incubated with OVA-BMDC proliferated greatly compared with those cultured with control BMDC, representing a greater than 11 fold induction. The proliferating cells observed on day 7 were TCR⁺CD4⁺CD8⁻ T cells, indicative of the OTII Tg T cell phenotype.

Significantly, when OTII T cells were cultured with OVA-BMDC in the presence of an antibody to block Sema6D (Sema6D Ab), the proliferation of the T cells was abrogated. While proliferation on day 6 and 7 was markedly reduced, the initial level of proliferation observed on day 2 was comparable to cultures with a control antibody (Ctrl Ab). Thus, while early survival may be unaffected, optimal proliferation and homeostasis of the Vβ5⁺ OTII T cells were inhibited by Sema6D blockade at both days 6 and 7.

The expression of Sema6D on in vitro activated OTII T cells was also examined and expression on both unactivated and activated T cells by day 7 was observed. BMDCs that were loaded (OVA-BMDC) or unloaded (BMDC) with whole OVA protein were cultured with purified OTII T cells in vitro. Prior to culture initiation, OTII T cells were labeled with CFSE. Antigen positive cultures were also treated with either a Sema6D blocking antibody or a control antibody. As expected, addition of blocking antibody significantly inhibited the detection of Sema6D expression compared with control antibody or unactivated cultures.

Finally, the ability of blocking Sema6D Ab to inhibit the appearance of an activated T cell phenotype was examined. Expression levels of CD25, CD62L, CD69, CD154 and CD44 were analyzed. For all the phenotypic markers analyzed, blocking Sema6D antibody inhibited the accumulation or appearance of activated OTII Tg T cells while isotype-control antibody did not. The low number of cells displaying an activated phenotype in the Sema6D Ab treated group may reflect an initial activation and proliferation that occurs in the presence of Sema6D Ab. Moreover, there does not appear to be reduced viability of CFSE^(bright) T cells lacking activation makers, suggesting that Sema6D Ab affects only stimulated T cells. These data indicate that Sema6D regulates DC mediated T cell proliferation, activation and survival.

Sema6D-Ig Inhibits BMDC Mediated T Cell Activation.

To further characterize the function of Sema6D, a hybrid of a cDNA fragment encoding the extracellular region of mouse Sema6D-6 (amino acids 1-652) and a human IgG1 fragment (hinge-CH2-CH3) was produced, resulting in a Sema6D-Ig fusion protein. This fusion protein was used along with the anti-Sema6D antibody in an experimental procedure as described herein. BMDCs that were loaded (OVA-BMDC) or unloaded (BMDC) with whole OVA protein were cultured with purified OTII T cells in vitro. Prior to culture initiation, OTII T cells were labeled with CFSE. Antigen positive cultures were also treated with a control antibody, a MHC class II blocking antibody, a Sema6D blocking antibody or the Sema6D-Ig fusion protein. At day 5 post culture initiation, the proliferation of CD4⁺ T cells was analyzed. Utilizing Sema6D-Ig as a blocking reagent administered to in vitro cultures, inhibition of BMDC mediated T cell proliferation was observed, as compared to a control antibody treated group (5.15% CFSE^(low)CD4⁺ vs. 29%). The level of inhibition with the Sema6D-Ig fusion protein was comparable to inhibition via the anti-Sema6D Ab. As a control, treatment with a blocking antibody for MHC II resulted in complete inhibition of T cell activation.

These studies demonstrate that activated T cells express high levels of Semaphorin 6D both in vitro and in vivo and that inhibition of Sema6D, via treatment with a blocking Ab or Sema6D-Ig, significantly inhibits dendritic cell mediated T cell activation. These data demonstrate that Sema6D represents an important novel receptor for the regulation of T cell immunity.

These studies further indicate that Sema6D inhibitors may reduce the survival of activated T cells only and do not appear to function as general inhibitors of T cell survival. In Sema6D Ab treated cultures (OVA-BMDC+Sema6D), the viability of non-dividing CFSE^(bright) and TCR⁺ or CD4⁺ cells did not appear to be affected when compared with T cells from naïve (BMDC) cultures (72.5 vs. 72.4%; and 66.1 vs. 67.2% respectively). Thus, in the case of autoimmunity, blocking Sema6D would allow for the specific targeting of activated autoimmune T cells while allowing unactivated, non-auotimmune T cells to persist. A similar method could be applied to transplant patients to induce a tolerizing effect on rejecting T cells. Alternatively, stimulating activated T cells via agonist ligand binding of Sema6D, could lead to enhanced vaccine efficacy or even enhanced tumor rejection via stimulation of anti-tumor T cells.

II. Blocking Sema6D with the Sema6D Ig Fusion Protein Caused a Delayed Inhibition of T Cell Activation

This was tested by assaying the phosphorylation of three T cell activating molecules, CrkL, LAT and CD3ζ. CD3ζ phosphorylation is an early event in T cell activation that occurs proximal to the T cell receptor. Its activation as indicated by phosphorylation is not altered by Sema6D-Ig inhibition. In the studies conducted, Sema6D was shown to regulate endogenous T cell signaling during late-stage activation. OTII T cells were co-cultured with DCs loaded with OVA antigen (OVA-DC) or unloaded DCs (DC). Antigen positive cultures were treated with Sema6D-Ig (S6D-Ig) or human IgG1 (hIgG1). OTII T cells co-cultured with DCs were analyzed by phosphor-specific flow cytometry for endogenous signaling pathways. FACS analysis of phosphorylated CrkL in TCR⁺ OTII T cells was carried out at days 3 and 6 of co-culture with DCs. FACS analysis of phosphorylated LAT in TCR⁺ OTII T cells was also carried out at days 3 and 6. FACS analysis of phosphorylated CD3ζ in TCR⁺ OTII T cells was also carried out at days 3 and 6 of co-culture.

Phosphorylation of CrkL is an indication of c-Abl activation, and it was inhibited by Sema6D-Ig inhibition but only at a late time point (day 6 but not day 3). LAT phosphorylation which lies downstream of c-Abl phosphorylation was inhibited by Sema6D-Ig at a late time point (day 6 but not day 3). These results indicate that Sema6D signaling is most relevant late during T cell activation. Further it lies upstream of c-Abl, CrkL and LAT phosphorylation but does not affect CD3ζ phosphorylation. Thus blocking Sema6D-Ig is a mechanism to block late T cell activation, which provides a different intervening point from most immune clinical biologics used in the market.

III. Expression of Sema6D on B Cells

This is of particular interest as recently anti-B cell antibodies have been effective in both reducing autoimmunity in people, and reducing B lymphoma growth. Sema6D was found to be expressed by B cells to a similar extent as T cells, in both mouse and human (FIGS. 1a,b ). Furthermore, expression was shown in four different types of leukemia (FIG. 1c ). Blocking Sema6D was shown to reduce T cell proliferation and B cell proliferation. This indicates that blocking Sema6D can reduce lymphocyte survival, which is important in the control of autoimmunity, but also in the control of transformed B and T lymphomas/leukemia.

Expression of Sema6D Protein in B Cells is Enhanced During an Immune Response.

To explore if the expression of Sema6D is enhanced during B cell activation (a state similar to auto-activated B cells implicated in autoimmune diseases such as systemic lupus and arthritis, and transformed B cells found in leukemia and lymphomas), B cells activated in vivo were tested with antigens and antigen presenting cells. DCs matured for 8 days in vitro were loaded with whole OVA protein and then transferred by i.v. injection with OTII TCR transgenic (OVA specific) T cells to recipient B6 mice. At day 4 post-transfer, recipient mouse splenocytes were isolated and analyzed by flow cytometry for the expression of Sema6D. Splenocytes were incubated with anti-CD45, -B220 and -Sema6D antibodies. B220⁺ CD45⁺ splenocytes were gated and analyzed for expression of Sema6D. The percentage of B220⁺ Sema6D⁺ cells was displayed for splenocytes from naïve and immune animals. These studies showed that in vivo activated B cells expressed significantly higher levels of Sema6D. In these experiments, B cells were marked with B220, and they showed elevated Sema6D after antigen stimulation. This suggests that Sema6D-Ig molecules might selectively target activated B cells and transformed B cells, but not naïve resting B cells.

Although the present invention has been described with reference to specific details of certain embodiments thereof, it is not intended that such details should be regarded as limitations upon the scope of the invention except as and to the extent that they are included in the accompanying claims.

Throughout this application, various patents, patent publications and non-patent publications are referenced. The disclosures of these patents and publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.

The foregoing is illustrative of the present invention, and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein.

REFERENCES

-   1. Keir, M. E., and A. H. Sharpe. 2005. The B7/CD28 costimulatory     family in autoimmunity. Immunol Rev 204:128. -   2. Greenwald, R. J., G. J. Freeman, and A. H. Sharpe. 2005. The B7     family revisited. Annu Rev Immunol 23:515. -   3. Girvin, A. M., M. C. Dal Canto, L. Rhee, B. Salomon, A.     Sharpe, J. A. Bluestone, and S. D. Miller. 2000. A critical role for     B7/CD28 costimulation in experimental autoimmune encephalomyelitis:     a comparative study using costimulatory molecule-deficient mice and     monoclonal antibody blockade. J Immunol 164:136. -   4. Salomon, B., and J. A. Bluestone. 2001. Complexities of CD28/B7:     CTLA-4 costimulatory pathways in autoimmunity and transplantation.     Annu Rev Immunol 19:225. -   5. Feldmann, M., and L. Steinman. 2005. Design of effective     immunotherapy for human autoimmunity. Nature 435:612, -   6. Quezada, S. A., L. Z. Jarvinen, E. F. Lind, and R. J.     Noelle. 2004. CD40/CD154 interactions at the interface of tolerance     and immunity. Annu Rev Immunol 22:307. -   7. Watts, T. H. 2005. TNF/TNFR family members in costimulation of T     cell responses. Annu Rev Immunol 23:23. -   8. Wong, A. W., W. J. Brickey, D. J. Taxman, H. W. van Deventer, W.     Reed, J. X. Gao, P. Zheng, Y. Liu, P. Li, J. S. Blum, K. P.     McKinnon, and J. P. Ting. 2003. CIITA-regulated plexin-A1 affects     T-cell-dendritic cell interactions. Nat Immunol 4:891. -   9. Tamagnone, L., S. Artigiani, H. Chen, Z. He, G. I. Ming, H.     Song, A. Chedotal, M. L. Winberg, C. S. Goodman, M. Poo, M.     Tessier-Lavigne, and P. M. Comoglio. 1999. Plexins are a large     family of receptors for transmembrane, secreted, and GPI-anchored     semaphorins in vertebrates. Cell 99:71. -   10. Castellani, V., and G. Rougon. 2002. Control of semaphorin     signaling. Curr Opin Neurobiol 12:532. -   11. Kikutani, H., and A. Kumanogoh, 2003. Semaphorins in     interactions between T cells and antigen-presenting cells. Nat Rev     Immunol 3:159. -   12. Kumanogoh, A., and H. Kikutani. 2003. Immune semaphorins: a new     area of semaphorin research. J Cell Sci 116:3463. -   13. Liu, B. P., and S. M. Strittmatter. 2001. Semaphorin-mediated     axonal guidance via Rho-related G proteins. Curr Opin Cell Biol     13:619. -   14. Tamagnone, L., and P. M. Comoglio. 2004. To move or not to move?     Semaphorin signalling in cell migration. EMBO Rep 5:356. -   15. Toyofuku, T., H. Zhang, A. Kumanogoh, N. Takegahara, M.     Yabuki, K. Harada, M. Hori, and H. Kikutani. 2004. Guidance of     myocardial patterning in cardiac development by Sema6D reverse     signalling. Nat Cell Biol 6:1204. -   16. Toyofuku, T., H. Zhang, A. Kumanogoh, N. Takegahara, F. Suto, J.     Kamei, K. Aoki, M. Yabuki, M. Hori, H. Fujisawa, and H.     Kikutani. 2004. Dual roles of Sema6D in cardiac morphogenesis     through region-specific association of its receptor, Plexin-A1, with     off-track and vascular endothelial growth factor receptor type 2.     Genes Dev 18:435. -   17. Turner, L. J., S. Nicholls, and A. Hall. 2004. The activity of     the plexin-A1 receptor is regulated by Rac. J Biol Chem 279:33199. -   18. Zanata, S. M., I. Hovatta, B. Rohm, and A. W. Puschel. 2002.     Antagonistic effects of Rnd1 and RhoD GTPases regulate receptor     activity in Semaphorin 3A-induced cytoskeletal collapse. J Neurosci     22:471. -   19. Zipfel, P. A., W. Zhang, M. Quiroz, and A. M. Pendergast. 2004.     Requirement for Abl kinases in T cell receptor signaling. Curr Biol     14:1222.

TABLE 1 Nucleotide and amino acid sequences of the Sema6D protein of the invention and a fusion protein of the invention. SEQ ID Accession No. Organism Definition NO: NM_020858 Homo sapiens Homo sapiens sema domain, transmembrane 21 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 1, mRNA. NP_065909 Homo sapiens semaphorin 6D isoform 1 precursor 22 NM_153616 Homo sapiens Homo sapiens sema domain, transmembrane 23 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 2, mRNA NP_705869 Homo sapiens semaphorin 6D isoform 2 precursor 24 NM_153617 Homo sapiens Homo sapiens sema domain, transmembrane 25 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 3, mRNA NP_705870 Homo sapiens semaphorin 6D isoform 3 precursor 26 NM_153618 Homo sapiens Homo sapiens sema domain, transmembrane 27 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 4, mRNA NP_705871 Homo sapiens semaphorin 6D isoform 4 precursor 28 NM_153619 Homo sapiens Homo sapiens sema domain, transmembrane 29 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 5, mRNA NP_705872 Homo sapiens semaphorin 6D isoform 5 precursor 30 NM_024966 Homo sapiens Homo sapiens sema domain, transmembrane 31 domain (TM), and cytoplasmic domain, (semaphorin) 6D (SEMA6D), transcript variant 6, mRNA NP_079242 Homo sapiens semaphorin 6D isoform 6 precursor 32 NM_172537 Mus musculus Mus musculus sema domain, transmembrane 33 domain (TM), and cytoplasmic domain, (semaphorin) 6D (Sema6d), transcript variant 1, mRNA n/a Mus musculus CDS of NM_172537 34 NP_766125 Mus musculus sema domain, transmembrane domain (TM), 35 and cytoplasmic domain, (semaphorin) 6D isoform 1 n/a Mus musculus CDS of NM_199238 36 NP_954708 Mus musculus sema domain, transmembrane domain (TM), 37 and cytoplasmic domain, (semaphorin) 6D isoform 2 n/a Mus musculus CDS of NM_199241 38 NP_954711 Mus musculus sema domain, transmembrane domain (TM), 39 and cytoplasmic domain, (semaphorin) 6D isoform 4 n/a Mus musculus CDS of NM_199239 47 NP_954709 Mus musculus sema domain, transmembrane domain (TM), 48 and cytoplasmic domain, (semaphorin) 6D isoform 5 n/a Mus musculus CDS of NM_199240 49 NP_954710 Mus musculus sema domain, transmembrane domain (TM), 50 and cytoplasmic domain, (semaphorin) 6D isoform 6 n/a Mus musculus CDS of Sema6D-6 51 BC098887 Danio rerio Danio rerio sema domain, transmembrane 52 domain (TM), and cytoplasmic domain, (semaphorin) 6D, mRNA AAH98887 Danio rerio Sema domain, transmembrane domain (TM), 53 and cytoplasmic domain, (semaphorin) 6D XM_230583 Rattus PREDICTED: Rattus norvegicus sema 54 norvegius domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D (predicted) (Sema6d_predicted), mRNA XP_230583 Rattus PREDICTED: similar to sema domain, 55 norvegius transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D isoform 4 XM_596649 Bos taurus PREDICTED: Bos taurus similar to 56 semaphorin 6D, transcript variant 5 (LOC518458), mRNA XP_596649 Bos taurus PREDICTED: similar to semaphorin 6D 57 isoform 5 n/a Artificial CDS of Murine sema6D-Ig fusion protein 58

TABLE 2  PCR and Sequencing primers Primer sequence SEQ ID NO: ATGGGGTTCCTTCTGCTTTGGTT (offset: 1; 23 nt) 7 CTAGTACGTGTACTTGTTCAGTGGTCTG (offset: 2997; 28 nt) 8 AAAGCAGAAGGAACCCCATGGTT (Rev. -838) 40 ACCAGGTAGCTAAGTGGGACTTCTG (For. 761-) 41 TGACACCCTGGCTTTCATCAAGT (For. 1161-) 42 AAAGTCTTGCATTGCATCACGTGAC (For. 1566-) 43 CCAATCAGATGGTCCACATGAA (For. 1964-) 44 ATGAAGAGCCACTCTGAGAAGGC (For. 2362-) 45 TAACCGGGAGGCATCTCTATAC (For. 2769-) 46 

What is claimed is:
 1. A fusion protein comprising the amino acid sequence of SEQ ID NO:2.
 2. A nucleic acid molecule comprising a nucleotide sequence encoding the fusion protein of claim
 1. 3. A nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:1.
 4. A composition comprising the fusion protein of claim 1 in a pharmaceutically acceptable carrier.
 5. A composition comprising the nucleic acid molecule of claim 2 in a pharmaceutically acceptable carrier.
 6. A composition comprising the nucleic acid molecule of claim 3 in a pharmaceutically acceptable carrier. 